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Yorodumi- PDB-5acp: W228R-Investigation of the impact from residues W228 and Y233 in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5acp | |||||||||
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Title | W228R-Investigation of the impact from residues W228 and Y233 in the metallo-beta-lactamase GIM-1 | |||||||||
Components | GIM-1 PROTEIN | |||||||||
Keywords | HYDROLASE / METALLO-BETA-LACTAMASE / GIM-1 / CARBAPENEMASE / ENZYME KINETICS / MIC | |||||||||
Function / homology | Function and homology information antibiotic catabolic process / beta-lactamase / hydrolase activity / metal ion binding Similarity search - Function | |||||||||
Biological species | PSEUDOMONAS AERUGINOSA (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å | |||||||||
Authors | Skagseth, S. / Carlsen, T.J. / Bjerga, G.E.K. / Spencer, J. / Samuelsen, O. / Leiros, H.-K.S. | |||||||||
Citation | Journal: Antimicrob.Agents Chemother. / Year: 2015 Title: Role of Residues W228 and Y233 in the Structure and Activity of Metallo-Beta-Lactamase Gim-1. Authors: Skagseth, S. / Carlsen, T.J. / Bjerga, G.E.K. / Spencer, J. / Samuelsen, O. / Leiros, H.S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5acp.cif.gz | 264 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5acp.ent.gz | 218.6 KB | Display | PDB format |
PDBx/mmJSON format | 5acp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5acp_validation.pdf.gz | 442.8 KB | Display | wwPDB validaton report |
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Full document | 5acp_full_validation.pdf.gz | 446.1 KB | Display | |
Data in XML | 5acp_validation.xml.gz | 19.1 KB | Display | |
Data in CIF | 5acp_validation.cif.gz | 26.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ac/5acp ftp://data.pdbj.org/pub/pdb/validation_reports/ac/5acp | HTTPS FTP |
-Related structure data
Related structure data | 5acqC 5acrC 5acsC 5actC 2yntS 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: 27473.160 Da / Num. of mol.: 2 / 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 PRARE / References: UniProt: Q704V1 #2: Chemical | #3: Chemical | ChemComp-MG / | #4: 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: 1.91 Å3/Da / Density % sol: 35.6 % / Description: NONE |
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Crystal grow | Details: 19.8% POLYETHYLENE GLYCOL (PEG) 10K AND 0.1 M SODIUM CACODYLATE, PH 6.5. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.24 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.24 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→41 Å / Num. obs: 28430 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 40.36 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 13 |
Reflection shell | Resolution: 1.98→2.05 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2YNT Resolution: 1.98→24.834 Å / SU ML: 0.23 / σ(F): 1.34 / Phase error: 24.87 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.98→24.834 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -13.0929 Å / Origin y: -48.9509 Å / Origin z: -11.1348 Å
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Refinement TLS group | Selection details: ALL |