+Open data
-Basic information
Entry | Database: PDB / ID: 2gg2 | ||||||
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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: 1 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 | 2gg2.cif.gz | 139 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gg2.ent.gz | 106.6 KB | Display | PDB format |
PDBx/mmJSON format | 2gg2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2gg2_validation.pdf.gz | 783.9 KB | Display | wwPDB validaton report |
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Full document | 2gg2_full_validation.pdf.gz | 784.4 KB | Display | |
Data in XML | 2gg2_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | 2gg2_validation.cif.gz | 25.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gg/2gg2 ftp://data.pdbj.org/pub/pdb/validation_reports/gg/2gg2 | HTTPS FTP |
-Related structure data
Related structure data | 2gg0C 2gg3C 2gg5C 2gg7C 2gg8C 2gg9C 2ggbC 2ggcC 1c27S C: citing same article (ref.) S: Starting model for refinement |
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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-U12 / | #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: 2.1 Å3/Da / Density % sol: 41.3 % |
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Crystal grow | Temperature: 298 K / Method: batch / pH: 7 Details: 10 mg/ml protein, 25% PEG 8000, 100 mM TRIS-HCl, 1-5 mM inhibitor, pH 7.0, batch, temperature 298K |
-Data collection
Diffraction |
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Diffraction source |
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Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2002 | ||||||||||||||||||
Radiation |
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Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 1→24.06 Å / Num. all: 122471 / Num. obs: 122471 / % possible obs: 93.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Rmerge(I) obs: 0.022 / Net I/σ(I): 23.1 | ||||||||||||||||||
Reflection shell | Resolution: 1→1.1 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.251 / Mean I/σ(I) obs: 5.5 / Num. unique all: 28624 / % possible all: 88.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1C27 Resolution: 1→24.06 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.974 / SU B: 0.551 / SU ML: 0.014 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.024 / ESU R Free: 0.024 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 11.162 Å2
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Refinement step | Cycle: LAST / Resolution: 1→24.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1→1.026 Å / Total num. of bins used: 20
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