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E. coli Statistics



This section contains several tables describing statistical data on E. coli derived or measured from several sources. These tables are periodically updated and are intended to provide CCDB users with sufficient or necessary details to help in cellular simulation programs or in explaining certain features of E. coli physiology and metabolism. The first table contains general statistics on E. coli dimensions, kinetics, components, copy numbers, concentrations and metabolism. The second table contains information derived from analyses of the E. coli genome and proteome as contained in the CCDB.



 General Statistics  

 1 

 Cell length  2 um or 2x10-6 m

 2 

 Cell diameter  0.8 um or 0.8x10-6 m

 3 

 Cell total volume  1x10-15 L or 1x10-18 m3

(other est. at 0.88x10-15 L)

 4 

 Cell aqueous volume  7 x 10-16 L

 5 

 Cell surface area  6x10-12 m2

 6 

 Cell wet weight  1x10-15 kg or 1x10-12 g

 7 

 Cell dry weight  3.0x10-16 kg or 3.0x10-13 g

 8 

 Periplasm volume  6.5x10-17 L

 9 

 Cytoplasm volume  6.7x10-16 L

 10 

 Envelope volume  1.6x10-16 L

 11 

 Nuclear (DNA+protein) volume  1.6x10-16 L

 12 

 Inner Membrane thickness  8x10-9 m

 13 

 Outer Membrane thickness  8x10-9 - 15x10-9 m

 14 

 Periplasm thickness  1x10-8 m

 15 

 Average size of protein  360 residues

 16 

 Average diameter of ave. protein  5 nm

 17 

 Average MW of protein  40 kD

 18 

 Average prot. oligomerization state  4 proteins/complex

 19 

 Average MW of protein entity  160 kD

 20 

 Average size of mRNA  1100 bases

 21 

 Average length of mRNA  370 nm

 22 

 Average MW of all RNAs  400 kD

 23 

 Average MW of single DNA  3.0x109 D or 3.0x106 kD

 24 

 Average MW of all DNA  7 x 106 kD

 25 

 Average length of DNA (chrom.)  1.55 mm

 26 

 Diameter of chromosome  490 um

 27 

 Diameter of condensed chromosome  17 um

 28 

 Spacing between small organics  3.6 nm/molecule

 29 

 Spacing between ions  2.1 nm/molecule

 30 

 Ave. spacing between proteins  7 nm/molecule

 31 

 Spacing between protein entities  9 nm/molecule

 32 

 Mean Velocity of 70 kD protein (cytoplasm)  3 nm/ms = 3x10-6 m/s

 33 

 Mean Velocity of 40 kD protein (cytoplasm)  5 nm/ms = 5x10-6 m/s

 34 

 Mean Velocity of 30 kD protein (cytoplasm)  7 nm/ms = 7x10-6 m/s

 35 

 Mean Velocity of 14 kD protein (cytoplasm)  10 nm/ms = 10x10-6 m/s

 36 

 Mean Velocity of small molecules (cytoplasm)  50 nm/ms = 5x10-5 m/s

 37 

 Mean Velocity of protein in H2O  27 nm/ms = 2.7x10-5 m/s

 38 

 Mean Velocity of small molecules in H2O  87 nm/ms = 8.7x10-5 m/s

 39 

 Concentration of protein in cell  200-320 mg/mL (5-8 mM)

 40 

 Concentration of RNA in cell  75-120 mg/mL (0.5-0.8 mM)

 41 

 Concentration of DNA in cell  11-18 mg/mL (5 nM)

 42 

 Volume occupied by water  70%

 43 

 Volume occupied by protein  17%

 44 

 Volume occupied by all RNA  6%

 45 

 Volume occupied by rRNA  5%

 46 

 Volume occupied by tRNA  0.8%

 47 

 Volume occupied by mRNA  0.2%

 48 

 Volume occupied by DNA  1%

 49 

 Volume occupied by ribosomes  8%

 50 

 Volume occupied by lipid  3%

 51 

 Volume occupied by LPS  1%

 52 

 Volume occupied by murein  1%

 53 

 Volume occupied by glycogen  1%

 54 

 Volume occupied by ions  0.3%

 55 

 Volume occupied by small organics  1%

 56 

 Translation rate  40 aa/sec

 57 

 RNA polymerase transcription rate  70 nt/sec

 Large Molecule Copy Numbers  

 1 

 Number of cell walls/cell  1

 2 

 Number of membranes/cell  2

 3 

 Number of chromosomes/cell  2.3 (at mid log phase)

 4 

 Number of mRNA/cell  4000

 5 

 Number of rRNA/cell  18,000

 6 

 Number of tRNA/cell  200,000

 7 

 Number of all RNA/cell  222,000

 8 

 Number of polysaccharides/cell  39,000

 9 

 Number of murein molecules/cell  240,000-700,000

 10 

 Number of lipopolysaccharide/cell  600,000

 11 

 Number of lipids/cell  25,000,000

 12 

 Number of all lipids/cell  25,000,000

 13 

 Number of phosphatidylethanolamine  18,500,000

 14 

 Number of phosphatidylglycerol  5,000,000

 15 

 Number of cardiolipin  1,200,000

 16 

 Number of phosphatidylserine  500,000

 17 

 Number of LPS (MW = 10kD)  600,000

 18 

 Average SA of lipid molecule  25 Ang2

 19 

 Fraction of lipid bilayer=lipid  40%

 20 

 Fraction of lipid bilayer=protein  60%

 21 

 Number of outer membrane proteins  300,000

 22 

 Number of porins (subset of OM)  60,000

 23 

 Number of lipoproteins (OM)  240,000

 24 

 Number of inner membrane proteins  200,000

 25 

 Number of nuclear proteins  100,000

 26 

 Number of cytoplasmic proteins  1,000,000 (excluding ribo proteins)

 27 

 Number of ribosomal proteins  900,000

 28 

 Number of periplasmic proteins  80,000

 29 

 Number of all proteins in cell  2,600,000

 30 

 Number of external proteins (flag/pili)  1,000,000

 31 

 Number of all proteins  3,600,000

 Statistics on Larger Molecule Complexes  

 1 

 Number of protein types to make flagella  42

 2 

 Length of flagella  10-20 um or ~15,000 nm

 3 

 Diameter of flagella  25 nm

 4 

 Number of protofilaments in flagellum  11

 5 

 Diameter of each fliC monomer  5 nm

 6 

 Number of fliC monomers in filament  3000x11=33,000

 7 

 Number of flagella/cell  10

 8 

 Number of fliC proteins  330,000

 9 

 Speed at which E. coli move  50 um/sec = 18 x10-5 km/h

 10 

 Number of protein types to make pilus  1

 11 

 Length of pili/fimbrae  200-2000 nm

 12 

 Diamter of pili  6.5 nm

 13 

 Number of papA/nm pilus  1.5

 14 

 Number of papA monomers/pilus  3000-30,000

 15 

 Number of pili/cell  100-300

 16 

 Number of papA/cell  300,000-900,000

 17 

 Number of ribosomes/cell  18,000

 18 

 Number of protein types to make ribosome  55

 19 

 Number rRNA types to make ribosome  3

 20 

 Number of proteins in 30S subunit  21

 21 

 Number of proteins in 50S subunit  34

 22 

 Number of rRNA in 30S subunit  1

 23 

 Number of rRNA in 50S subunit  2

 24 

 Length of all rRNA  5520 nt

 25 

 MW of ribosome  2700 kD

 26 

 MW of RNA component  1700 kD

 27 

 MW of protein component  1000 kD

 28 

 Diameter of ribosome  20 nm

 29 

 Volume of ribosome  4.2 x 10-24 m3

 Small Molecule Copy Numbers  

 1 

 Number of water molecules/cell  2.34x1010 (23.4 billion)

 2 

 Number of ions/cell  120,000,000 (300 mM)

 3 

 Number of small organics/cell  18,000,000 (40-50 mM)

 4 

 Number of K ions  90,000,000 (200-250 mM)

 5 

 Number of Na ions  2,000,000 (5 mM)

 6 

 Na (in): Na (out)  1:20 (in concentration)

 7 

 Number of Ca ions  2,300,000 (6 mM)

 8 

 Number of free Ca ions  40 (100 nM)

 9 

 Number of Cl ions  2,400,000 (6 mM)

 10 

 Number of Mg ions  4,000,000 (10 mM)

 11 

 Number of Fe ions  7,000,000 (18 mM)

 12 

 Number of Mn ions  1,700,000 (4 mM)

 13 

 Number of Zn ions  1,700,000 (4 mM)

 14 

 Number of Mo ions  1,700,000 (4 mM)

 15 

 Number of Cu ions  1,700,000 (4 mM)

 16 

 Number of PO4 ions  2,000,000 (5 mM)

 17 

 Number of glucose/cell  200,000-400,000 (0.5-1 mM)

 18 

 Number of PEP/cell  1,100,000 (2.8 mM)

 19 

 Number of pyruvate/cell  370,000 (0.9 mM)

 20 

 Number of gluc-6-PO4/cell  20,000 (0.05 mM)

 21 

 Number of ATP/cell  500,000 3,000,000 (1.3-7.0 mM)

 22 

 Number of ADP/cell  70,000 (0.17 mM)

 23 

 Number of NADP/cell  240,000 (0.63 mM)

 24 

 Number of NADPH/cell  220,000 (0.56 mM)

 25 

 Number of all amino acids/cell  6,000,000 (1.5 mM)

 26 

 Number of free Alanine/cell  350,000 (0.8 mM)

 27 

 Number of free Cysteine/cell  80,000 (0.2 mM)

 28 

 Number of free Aspartate/cell  530,000 (1.34 mM)

 29 

 Number of free Glutamate/cell  200,000 (0.5 mM)

 30 

 Number of free Phenylalanine/cell  170,000 (0.4 mM)

 31 

 Number of free Glycine/cell  350,000 (0.8 mM)

 32 

 Number of free Histidine/cell  80,000 (0.2 mM)

 33 

 Number of free Isoleucine/cell  200,000 (0.5 mM)

 34 

 Number of free Lysine/cell  190,000 (0.46 mM)

 35 

 Number of free Leucine/cell  300,000 (0.7 mM)

 36 

 Number of free Methionine/cell  40,000 (0.1 mM)

 37 

 Number of free Asparagine/cell  200,000 (0.5 mM)

 38 

 Number of free Proline/cell  200,000 (0.5 mM)

 39 

 Number of free Glutamine/cell  200,000 (0.5 mM)

 40 

 Number of free Arginine/cell  170,000 (0.4 mM)

 41 

 Number of free Serine/cell  300,000 (0.7 mM)

 42 

 Number of free Threonine/cell  1,400,000 (3.49 mM)

 43 

 Number of free Valine/cell  240,000 (0.6 mM)

 44 

 Number of free Tryptophan/cell  80,000 (0.2 mM)

 45 

 Number of free Tyrosine/cell  300,000 (0.7 mM)

 46 

 Osmotic pressure (pushing out)  75 lb/in2

 E. coli Metabolism  

 1 

 1 glucose generates (total)  36-38 ATP

 2 

 glycolysis yields  6-8 ATP

 3 

 oxidation of pyruvate yields  6 ATP

 4 

 Krebs cycle/e- transport yields  24 ATP

 5 

 Number ATP to make 1 DNA  72,289,000

 6 

 Number ATP to make 1 protein (360 aa)  1500

 7 

 Number ATP to make 1 lipid  7

 8 

 Number ATP to make 1 polysaccharide  2000

 9 

 Number ATP to make 1 RNA (1000 nt)  2000

 10 

 Number ATP to make 1 cell  55 billion ATP

 11 

 Number Glucose molecules consumed  1.4 billion molecules

 12 

 Cell division rate  1 division/30 minutes


   
E. coli Statistics References

  1)   http://old.jccc.net/~pdecell/cellresp/whyatp.html
  2)   Garrett, R.H., and Grisham, C.M. Biochemistry, 2nd Edition (2002), pg. 32
  3)   http://microvet.arizona.edu/Courses/MIC328/328%20Topic%201%20notes.html
  4)   Goodsell, D.S. (1991) Inside a Living Cell, Trends Biochem Sci. 16, 203-206.
  5)   Neidhardt, F.C. et al. (1987) Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology Vol. 1. American Society for Microbiology.
  6)   Nanninga N., ed. (1985) Molecular Cytology of Escherichia coli, Academic Press
  7)   Ingraham, J.L., Maaloe, O. and Neidhardt, F.C. (1983) Growth of the Bacterial Cell, Sinauer Association
  8)   Albe, K.R., Butler, M.H. and Wright, B.E. (1990) J. Theor. Biol. 143, 163-195.
  9)   Rohwer, J.M. et al. (2000) Understanding Glucose Transport, J. Biol. Chem. 275, 34909-34921.
  10)   Elowitz, M.B. et al. (1999) Protein Mobility in the Cytoplasm of E. coli, J. Bacteriol 181, 197-203.
  11)   Chassagnole, C. et al. (2001) Control of the Threonine Synthesis Pathway in E. coli, Biochem. J. 356, 433-444.
  12)   Zimmereman, S.B. and Trach, S.O. (1991) Estimation of Macromolecular Concentrations in E. coli, J. Mol. Biol. 222, 599-620.
  13)   http://www.bact.wisc.edu/MicrotextBook/BacterialStructure/introduction.html


   
Codon Usage Table

Codon Amino Acid Relative Abundance
per Amino Acid
Relative Frequency
per 1000 Codons




The sequence of E. coli reveals 4441 open reading frames corresponding to 4322 proteins and 122 rRNAs and tRNAs.Of these, only two thirds are of known function.The entire complement of proteins in E. coli can be classified into 12 molecular functions. Among the ORFs there are 609 nucleic acid binding proteins, 247 transcription regulatory proteins, 59 proteins wiith chaperonin activity, 19 proteins with motor activity, 1656 proteins with catalytic activity, 687 proteins with transporter activity, 1079 binding proteins, 71 with structure-only roles, 2 toxins, 4 enzyme regulators, 6 defense/immunity proteins and 91 proteins with signal transducer activity . Considerabledata is accumulating on the proteins, their localization and expression. Presently, the three-dimensional structure of over 532 (12%) are available on the PDB database and an additional 770 (18%) have been modeled. However, a much large number of homologous proteins have also had their X-ray or NMR structures determined. As of Aug. 1, 2003, the number of PSI-BLAST fold assignments for E. coli has increased to 2150 proteins or approximately 49% of the known E. coli ORFs.
   
CyberCell Database Statistics

  

 Item

 Number

  1 

 Number of Protein Coding Genes  4252

  2 

 Number of X-Ray Structures    478

  3 

 Number of NMR Structures      65

  4 

 Number of Model Structures    770

  5 

 Number without 3D Structures  2976

  6 

 Number of Cytoplasmic Proteins  2790

  7 

 Number of Periplasmic Proteins    152

  8 

 Number of Membrane Proteins    1053

  9 

 Number with EC Numbers    933

 10 

 Number with Incomplete EC Numbers     396

 11 

 Number with No EC Numbers  2923

 12 

 Number with Quaternary Structures  1340

 13 

 Number of Interacting Partners  1421

 14 

 Number with Unknown Functions  432

 15 

 Number of Essential Genes    297

 16 

 Number of Non Essential Genes  2052

 17 

 Number of Unknown Importance  1839

 18 

 Number with Homologs in Model Organisms   1067

 19 

 Number with Paralogs    4232

 20 

 Number with Signal Peptides    792

 21 

 Number with Met Cleavage  3751

 22 

 Number of Translated Proteins  4190

 23 

 Number of Post-Translated Proteins  3810

 24 

 Total Number of Translated + Mature Proteins  7941