+Open data
-Basic information
Entry | Database: PDB / ID: 7xhx | |||||||||
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Title | Crystal structure of metallo-beta-lactamase IMP-6 | |||||||||
Components | Beta-lactamase | |||||||||
Keywords | HYDROLASE / Metallo-beta-lactamase / Carbapenemase / Zinc protein / Antimicrobial protein | |||||||||
Function / homology | Function and homology information antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic / zinc ion binding Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | |||||||||
Authors | Yamamoto, K. / Tanaka, H. / Kurisu, G. / Nakano, R. / Yano, H. / Sakai, H. | |||||||||
Funding support | Japan, 1items
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Citation | Journal: J.Biochem. / Year: 2022 Title: Structural insights into the substrate specificity of IMP-6 and IMP-1 metallo-beta-lactamases. Authors: Yamamoto, K. / Tanaka, H. / Kurisu, G. / Nakano, R. / Yano, H. / Sakai, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xhx.cif.gz | 188.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xhx.ent.gz | 146.9 KB | Display | PDB format |
PDBx/mmJSON format | 7xhx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7xhx_validation.pdf.gz | 3.9 MB | Display | wwPDB validaton report |
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Full document | 7xhx_full_validation.pdf.gz | 3.9 MB | Display | |
Data in XML | 7xhx_validation.xml.gz | 34.3 KB | Display | |
Data in CIF | 7xhx_validation.cif.gz | 49.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xh/7xhx ftp://data.pdbj.org/pub/pdb/validation_reports/xh/7xhx | HTTPS FTP |
-Related structure data
Related structure data | 7xhwC 1ddkS 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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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 27125.119 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: blaIMP-6 / Production host: Escherichia coli (E. coli) / References: UniProt: K4PWX3, beta-lactamase #2: Chemical | ChemComp-ZN / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.31 Å3/Da / Density % sol: 46.73 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.1 M sodium acetate, 0.2 M ammonium acetate, 17% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 14, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 112203 / % possible obs: 100 % / Redundancy: 6.76 % / CC1/2: 0.997 / Net I/σ(I): 13.73 |
Reflection shell | Resolution: 1.7→1.79 Å / Num. unique obs: 17827 / CC1/2: 0.941 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DDK Resolution: 1.7→48.3 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.534 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.106 / 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: 38.136 Å2
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Refinement step | Cycle: 1 / Resolution: 1.7→48.3 Å
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Refine LS restraints |
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