+Open data
-Basic information
Entry | Database: PDB / ID: 2ggb | ||||||
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Title | Novel bacterial methionine aminopeptidase inhibitors | ||||||
Components | Methionine aminopeptidase | ||||||
Keywords | HYDROLASE / methionine amino peptidase / pita-bread fold / MAP inhibitor / antibacterial | ||||||
Function / homology | Function and homology information initiator methionyl aminopeptidase activity / methionyl aminopeptidase / metalloaminopeptidase activity / ferrous iron binding / proteolysis / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli K12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å | ||||||
Authors | Evdokimov, A.G. / Pokross, M.E. / Walter, R.L. / Mekel, M. | ||||||
Citation | Journal: Proteins / Year: 2007 Title: Serendipitous discovery of novel bacterial methionine aminopeptidase inhibitors. Authors: Evdokimov, A.G. / Pokross, M. / Walter, R.L. / Mekel, M. / Barnett, B.L. / Amburgey, J. / Seibel, W.L. / Soper, S.J. / Djung, J.F. / Fairweather, N. / Diven, C. / Rastogi, V. / Grinius, L. / ...Authors: Evdokimov, A.G. / Pokross, M. / Walter, R.L. / Mekel, M. / Barnett, B.L. / Amburgey, J. / Seibel, W.L. / Soper, S.J. / Djung, J.F. / Fairweather, N. / Diven, C. / Rastogi, V. / Grinius, L. / Klanke, C. / Siehnel, R. / Twinem, T. / Andrews, R. / Curnow, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ggb.cif.gz | 70.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ggb.ent.gz | 50.5 KB | Display | PDB format |
PDBx/mmJSON format | 2ggb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ggb_validation.pdf.gz | 722.6 KB | Display | wwPDB validaton report |
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Full document | 2ggb_full_validation.pdf.gz | 728.9 KB | Display | |
Data in XML | 2ggb_validation.xml.gz | 9.3 KB | Display | |
Data in CIF | 2ggb_validation.cif.gz | 12.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gg/2ggb ftp://data.pdbj.org/pub/pdb/validation_reports/gg/2ggb | HTTPS FTP |
-Related structure data
Related structure data | 2gg0SC 2gg2C 2gg3C 2gg5C 2gg7C 2gg8C 2gg9C 2ggcC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 29239.643 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12 / Gene: map / Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0AE18, methionyl aminopeptidase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-NA / | #4: Chemical | ChemComp-U17 / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.66 % |
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Crystal grow | Temperature: 298 K / pH: 7 Details: 10 mg/ml protein, 25% PEG 8000, 100 mM TRIS-HCl, 1-5 mM inhibitor, batch, pH 7.0, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2002 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.13→30.73 Å / Num. all: 13433 / Num. obs: 13433 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rmerge(I) obs: 0.021 / Net I/σ(I): 25.4 |
Reflection shell | Resolution: 2.13→2.25 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.082 / Mean I/σ(I) obs: 10.9 / Num. unique all: 2012 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2GG0 Resolution: 2.13→30.73 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.91 / SU B: 13.179 / SU ML: 0.184 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.304 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.039 Å2
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Refinement step | Cycle: LAST / Resolution: 2.13→30.73 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.13→2.185 Å / Total num. of bins used: 20
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