+Open data
-Basic information
Entry | Database: PDB / ID: 4a6v | ||||||
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Title | X-ray structures of oxazole hydroxamate EcMetAp-Mn complexes | ||||||
Components | METHIONINE AMINOPEPTIDASE | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information : / initiator methionyl aminopeptidase activity / methionyl aminopeptidase / metalloaminopeptidase activity / transition metal ion binding / proteolysis Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å | ||||||
Authors | Huguet, F. / Melet, A. / AlvesdeSousa, R. / Lieutaud, A. / Chevalier, J. / Deschamps, P. / Tomas, A. / Leulliot, N. / Pages, J.M. / Artaud, I. | ||||||
Citation | Journal: Chemmedchem / Year: 2012 Title: Hydroxamic Acids as Potent Inhibitors of Fe(II) and Mn(II) E. Coli Methionine Aminopeptidase: Biological Activities and X-Ray Structures of Oxazole Hydroxamate-Ecmetap-Mn Complexes. Authors: Huguet, F. / Melet, A. / Alves De Sousa, R. / Lieutaud, A. / Chevalier, J. / Maigre, L. / Deschamps, P. / Tomas, A. / Leulliot, N. / Pages, J.M. / Artaud, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4a6v.cif.gz | 254.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4a6v.ent.gz | 204.1 KB | Display | PDB format |
PDBx/mmJSON format | 4a6v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4a6v_validation.pdf.gz | 1012.6 KB | Display | wwPDB validaton report |
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Full document | 4a6v_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 4a6v_validation.xml.gz | 32.1 KB | Display | |
Data in CIF | 4a6v_validation.cif.gz | 49.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a6/4a6v ftp://data.pdbj.org/pub/pdb/validation_reports/a6/4a6v | HTTPS FTP |
-Related structure data
Related structure data | 4a6wC 2matS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 29441.916 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: BL21(DE3) References: UniProt: C6EAB7, UniProt: A0A140NFG5*PLUS, methionyl aminopeptidase #2: Chemical | ChemComp-MN / #3: Chemical | ChemComp-CO3 / | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 40.05 % / Description: NONE |
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Crystal grow | Method: vapor diffusion / pH: 7.5 Details: VAPOUR DIFFUSION 17 TO 25 % PEG 8000, HEPES, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.7 2.1 | |||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL | |||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.46→37.06 Å / Num. obs: 80700 / % possible obs: 98.3 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 7.1 | |||||||||
Reflection shell | Resolution: 1.46→1.54 Å / Redundancy: 4 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 3.4 / % possible all: 97.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2MAT Resolution: 1.46→74.11 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.755 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.767 Å2
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Refinement step | Cycle: LAST / Resolution: 1.46→74.11 Å
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Refine LS restraints |
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