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Open data
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Basic information
Entry | Database: PDB / ID: 2gg3 | ||||||
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Title | Novel bacterial methionine aminopeptidase inhibitors | ||||||
![]() | Methionine aminopeptidase | ||||||
![]() | HYDROLASE / methionine amino peptidase / pita-bread fold / MAP inhibitor / antibacterial | ||||||
Function / homology | ![]() initiator methionyl aminopeptidase activity / methionyl aminopeptidase / metalloaminopeptidase activity / ferrous iron binding / proteolysis / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Evdokimov, A.G. / Pokross, M.E. / Walter, R.L. / Mekel, M. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 136.5 KB | Display | ![]() |
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PDB format | ![]() | 104.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 439.7 KB | Display | ![]() |
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Full document | ![]() | 440.1 KB | Display | |
Data in XML | ![]() | 15.7 KB | Display | |
Data in CIF | ![]() | 24.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2gg0C ![]() 2gg2SC ![]() 2gg5C ![]() 2gg7C ![]() 2gg8C ![]() 2gg9C ![]() 2ggbC ![]() 2ggcC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() ![]() | ||||||
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#2: Chemical | #3: Chemical | ChemComp-NA / | #4: Chemical | ChemComp-U13 / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.81 % |
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Crystal grow | Temperature: 298 K / pH: 7 Details: 10 mg/ml protein, 25% PEG 8000, 100 mM TRIS-HCl, batch, pH 7.0, temperature 298K |
-Data collection
Diffraction |
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||
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: 1.45→24.92 Å / Num. all: 40960 / Num. obs: 40960 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.031 / Net I/σ(I): 18.7 | |||||||||
Reflection shell | Resolution: 1.45→1.55 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.235 / Mean I/σ(I) obs: 4.23 / Num. unique all: 6408 / % possible all: 85.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2GG2 Resolution: 1.45→24.92 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.971 / SU B: 2.055 / SU ML: 0.037 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.073 / ESU R Free: 0.061 / 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: 15.946 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→24.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.452→1.49 Å / Total num. of bins used: 20
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