+Open data
-Basic information
Entry | Database: PDB / ID: 4d1w | ||||||
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Title | A H224Y mutant for VIM-7 from Pseudomonas aeruginosa | ||||||
Components | METALLO-B-LACTAMASE | ||||||
Keywords | HYDROLASE / RESIDUE DETERMINANTS / LIGAND INTERACTION | ||||||
Function / homology | Function and homology information antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding Similarity search - Function | ||||||
Biological species | PSEUDOMONAS AERUGINOSA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Leiros, H.-K.S. / Skagseth, S. / Edvardsen, K.S.W. / Lorentzen, M.S. / Bjerga, G.E.K. / Leiros, I. / Samuelsen, O. | ||||||
Citation | Journal: Antimicrob.Agents Chemother. / Year: 2014 Title: His224 Alters the R2 Drug Binding Site and Phe218 Influences the Catalytic Efficiency in the Metallo-Beta-Lactamase Vim-7. Authors: Leiros, H.-K.S. / Skagseth, S. / Edvardsen, K.S.W. / Lorentzen, M.S. / Bjerga, G.E.K. / Leiros, I. / Samuelsen, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4d1w.cif.gz | 115.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4d1w.ent.gz | 87.7 KB | Display | PDB format |
PDBx/mmJSON format | 4d1w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4d1w_validation.pdf.gz | 434.1 KB | Display | wwPDB validaton report |
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Full document | 4d1w_full_validation.pdf.gz | 435.1 KB | Display | |
Data in XML | 4d1w_validation.xml.gz | 13.6 KB | Display | |
Data in CIF | 4d1w_validation.cif.gz | 20.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d1/4d1w ftp://data.pdbj.org/pub/pdb/validation_reports/d1/4d1w | HTTPS FTP |
-Related structure data
Related structure data | 4d1tC 4d1uC 4d1vC 2y8bS 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: 28214.869 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: Q840P9 | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 40.14 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→30 Å / Num. obs: 43649 / % possible obs: 96.6 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 12.8 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 1.4→1.48 Å / Redundancy: 2 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 0 / % possible all: 86.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2Y8B Resolution: 1.4→25 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.302 / SU ML: 0.024 / Cross valid method: THROUGHOUT / ESU R: 0.05 / ESU R Free: 0.05 / 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: 14.582 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→25 Å
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Refine LS restraints |
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