+Open data
-Basic information
Entry | Database: PDB / ID: 7aez | |||||||||
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Title | Crystal structure of the metallo-beta-lactamase NDM-7 with 407 | |||||||||
Components | Metallo-beta-lactamase NDM-7 | |||||||||
Keywords | HYDROLASE / HYDROLASE METALLO-BETA-LACTAMASE ANTIBIOTIC RESISTANCE | |||||||||
Function / homology | Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 2-ETHOXYETHANOL / Chem-R8W / Metallo-beta-lactamase NDM-7 Function and homology information | |||||||||
Biological species | Klebsiella pneumoniae (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.018 Å | |||||||||
Authors | Brem, J. / Schofield, C.J. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: To Be Published Title: Not available yet Authors: Brem, J. / Schofield, C.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7aez.cif.gz | 165.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7aez.ent.gz | 132 KB | Display | PDB format |
PDBx/mmJSON format | 7aez.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7aez_validation.pdf.gz | 790 KB | Display | wwPDB validaton report |
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Full document | 7aez_full_validation.pdf.gz | 790.8 KB | Display | |
Data in XML | 7aez_validation.xml.gz | 15.1 KB | Display | |
Data in CIF | 7aez_validation.cif.gz | 23.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ae/7aez ftp://data.pdbj.org/pub/pdb/validation_reports/ae/7aez | HTTPS FTP |
-Related structure data
Related structure data | 4tzfS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 24400.400 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: CYS208 is sp2 hybridised at CA / Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaNDM-7 / Production host: Escherichia coli (E. coli) / Strain (production host): pLyS / References: UniProt: X5CZV5 |
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-Non-polymers , 7 types, 340 molecules
#2: Chemical | ChemComp-R8W / | ||||||||||
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#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-EDO / | #6: Chemical | ChemComp-NA / | #7: Chemical | ChemComp-ETX / | #8: Water | ChemComp-HOH / | |
-Details
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: 2.11 Å3/Da / Density % sol: 41.82 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1M Bis Tris pH 5.5 25% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 7, 2017 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.01843→27.97 Å / Num. obs: 97817 / % possible obs: 92.2 % / Redundancy: 11.4 % / Biso Wilson estimate: 8.56 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.017 / Rrim(I) all: 0.06 / Net I/σ(I): 24.8 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4TZF Resolution: 1.018→27.719 Å / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 9.59 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 50.2 Å2 / Biso mean: 13.1449 Å2 / Biso min: 6.05 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.018→27.719 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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