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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 |
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. |
|
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 |
Original Designer: Bahram Habibi-Nazhad (BHN) (Last Update: Aug 01, 2008) |