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Yorodumi- PDB-7rpd: X-ray crystal structure of OXA-24/40 V130D in complex with ertapenem -
+Open data
-Basic information
Entry | Database: PDB / ID: 7rpd | |||||||||
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Title | X-ray crystal structure of OXA-24/40 V130D in complex with ertapenem | |||||||||
Components | Beta-lactamase | |||||||||
Keywords | HYDROLASE/Inhibitor / acyl-enzyme complex / carbapenemase / HYDROLASE / HYDROLASE-Inhibitor complex | |||||||||
Function / homology | Function and homology information penicillin binding / cell wall organization / beta-lactamase activity / beta-lactamase Similarity search - Function | |||||||||
Biological species | Acinetobacter baumannii (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | |||||||||
Authors | Powers, R.A. / Mitchell, J.M. / June, C.M. | |||||||||
Funding support | United States, 2items
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Citation | Journal: J.Biol.Chem. / Year: 2022 Title: Conformational flexibility in carbapenem hydrolysis drives substrate specificity of the class D carbapenemase OXA-24/40. Authors: Mitchell, J.M. / June, C.M. / Baggett, V.L. / Lowe, B.C. / Ruble, J.F. / Bonomo, R.A. / Leonard, D.A. / Powers, R.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7rpd.cif.gz | 68.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7rpd.ent.gz | 47.9 KB | Display | PDB format |
PDBx/mmJSON format | 7rpd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7rpd_validation.pdf.gz | 812.9 KB | Display | wwPDB validaton report |
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Full document | 7rpd_full_validation.pdf.gz | 814.7 KB | Display | |
Data in XML | 7rpd_validation.xml.gz | 12.3 KB | Display | |
Data in CIF | 7rpd_validation.cif.gz | 17.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rp/7rpd ftp://data.pdbj.org/pub/pdb/validation_reports/rp/7rpd | HTTPS FTP |
-Related structure data
Related structure data | 7rp8C 7rp9C 7rpaC 7rpbC 7rpcC 7rpeC 7rpfC 7rpgC 3paeS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 27690.809 Da / Num. of mol.: 1 / Mutation: V130D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) Gene: blaOXA-33, bla-OXA-40, blaOXA-24, blaOXA-40, oxa-24, oxa40, SI89_16690 Plasmid: pET24a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8RLA6, beta-lactamase | ||||||||
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#2: Chemical | ChemComp-1RG / ( | ||||||||
#3: Chemical | #4: Chemical | ChemComp-SO4 / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | Has protein modification | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.1 Å3/Da / Density % sol: 69.97 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M TRIS HCL, 2.0 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.1272 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 12, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1272 Å / Relative weight: 1 |
Reflection | Resolution: 1.948→102.696 Å / Num. obs: 33705 / % possible obs: 98.7 % / Redundancy: 7.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.034 / Rrim(I) all: 0.095 / Net I/σ(I): 12.3 / Num. measured all: 247955 |
Reflection shell | Resolution: 1.948→1.955 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.909 / Num. unique obs: 339 / CC1/2: 0.817 / Rpim(I) all: 0.359 / Rrim(I) all: 0.979 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3PAE Resolution: 1.95→72.62 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.954 / SU B: 4.146 / SU ML: 0.106 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.112 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 113.32 Å2 / Biso mean: 43.455 Å2 / Biso min: 25.05 Å2
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Refinement step | Cycle: final / Resolution: 1.95→72.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→1.999 Å / Rfactor Rfree error: 0
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