+Open data
-Basic information
Entry | Database: PDB / ID: 7vvi | |||||||||
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Title | OXA-58 crystal structure of acylated meropenem complex | |||||||||
Components | Beta-lactamase | |||||||||
Keywords | HYDROLASE / OXA / multi-drug resistance / Complex / Degradation | |||||||||
Function / homology | Function and homology information penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | |||||||||
Biological species | Acinetobacter baumannii (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | |||||||||
Authors | Saino, H. / Sugiyabu, T. / Miyano, M. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: to be published Title: OXA-58 crystal structure of acylated meropenem complex Authors: Saino, H. / Okimoto, N. / Otsuka, T. / Sugiyabu, T. / Sasaki, I. / Ueno, G. / Oouchi, M. / Yamamoto, M. / Ishii, K. / Taiji, M. / Miyano, M. #1: Journal: PLoS One / Year: 2015 Title: Crystal Structure of OXA-58 with the Substrate-Binding Cleft in a Closed State: Insights into the Mobility and Stability of the OXA-58 Structure. Authors: Saino, H. / Sugiyabu, T. / Ueno, G. / Yamamoto, M. / Ishii, Y. / Miyano, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7vvi.cif.gz | 81.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vvi.ent.gz | 52.5 KB | Display | PDB format |
PDBx/mmJSON format | 7vvi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7vvi_validation.pdf.gz | 743.9 KB | Display | wwPDB validaton report |
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Full document | 7vvi_full_validation.pdf.gz | 745.2 KB | Display | |
Data in XML | 7vvi_validation.xml.gz | 15.1 KB | Display | |
Data in CIF | 7vvi_validation.cif.gz | 23.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vv/7vvi ftp://data.pdbj.org/pub/pdb/validation_reports/vv/7vvi | HTTPS FTP |
-Related structure data
Related structure data | 5bohS S: Starting model for refinement |
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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
#1: Protein | Mass: 28778.896 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: blaOXA-58, bla-oxa-58, bla-oxa58 / Plasmid: pCold I / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2TR58, beta-lactamase |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-MER / ( |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.87 % / Description: Thin plate |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: LiSO4, HEPES-Na, Meropenem soaking |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 22, 2014 |
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→19.29 Å / Num. obs: 685938 / % possible obs: 99.52 % / Redundancy: 6.9 % / Biso Wilson estimate: 12.56 Å2 / CC1/2: 0.628 / CC star: 0.878 / Rmerge(I) obs: 0.7342 / Rpim(I) all: 0.2962 / Rsym value: 0.794 / Net I/σ(I): 158.17 |
Reflection shell | Resolution: 1.4→1.45 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.7758 / Mean I/σ(I) obs: 18.01 / Num. unique obs: 66353 / CC1/2: 0.132 / CC star: 0.482 / Rpim(I) all: 0.3234 / Rrim(I) all: 0.8451 / % possible all: 99.37 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5BOH Resolution: 1.4→19.29 Å / Cross valid method: FREE R-VALUE / σ(F): 1.27 / Phase error: 16.3904 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.51 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→19.29 Å
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Refine LS restraints |
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LS refinement shell |
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