+Open data
-Basic information
Entry | Database: PDB / ID: 5zr8 | ||||||
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Title | Crystal Structure Of NDM-1 Metallo-beta-lactamase | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information antibiotic catabolic process / beta-lactamase / hydrolase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Wachino, J. | ||||||
Citation | Journal: To Be Published Title: Crystal Structure Of NDM-1 Metallo-beta-lactamase Authors: Wachino, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zr8.cif.gz | 112.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zr8.ent.gz | 84.7 KB | Display | PDB format |
PDBx/mmJSON format | 5zr8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5zr8_validation.pdf.gz | 445.9 KB | Display | wwPDB validaton report |
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Full document | 5zr8_full_validation.pdf.gz | 448.5 KB | Display | |
Data in XML | 5zr8_validation.xml.gz | 23.5 KB | Display | |
Data in CIF | 5zr8_validation.cif.gz | 35.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zr/5zr8 ftp://data.pdbj.org/pub/pdb/validation_reports/zr/5zr8 | HTTPS FTP |
-Related structure data
Related structure data | 4eybS 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: 26045.295 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) Gene: blaNDM-1, bla NDM-1, AM434_27040, APU18_05360, AZ95_0035, BET08_16280, BVL39_26630, CA268_28970, ECS01_0033, MS6198_A142, NDM1Dok01_N0175, pNDM102337_147, pNDM10505_149 Production host: Escherichia coli (E. coli) / References: UniProt: E5KIY2 #2: Chemical | ChemComp-ZN / #3: Chemical | #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: 1.96 Å3/Da / Density % sol: 37.25 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2M Ammonium Sulfate, 0.1 M Bis-Tris [pH 6.1], 25% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Dec 9, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→53.56 Å / Num. obs: 66267 / % possible obs: 100 % / Redundancy: 10.6 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 18.6 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.439 / Num. unique obs: 9562 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4eyb Resolution: 1.5→53.56 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.015 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.065 / ESU R Free: 0.065 / 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: 14.09 Å2
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Refinement step | Cycle: 1 / Resolution: 1.5→53.56 Å
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