+Open data
-Basic information
Entry | Database: PDB / ID: 3zr9 | ||||||
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Title | Structure of New Delhi Metallo-Beta-lactamase 1 (NDM-1) | ||||||
Components | BETA-LACTAMASE NDM-1 | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding Similarity search - Function | ||||||
Biological species | KLEBSIELLA PNEUMONIAE (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å | ||||||
Authors | Green, V.L. / Verma, A. / Owens, R.J. / Phillips, S.E.V. / Carr, S.B. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2011 Title: Structure of New Delhi Metallo-Beta-Lactamase 1 (Ndm-1). Authors: Green, V.L. / Verma, A. / Owens, R.J. / Phillips, S.E. / Carr, S.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zr9.cif.gz | 103.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zr9.ent.gz | 78.2 KB | Display | PDB format |
PDBx/mmJSON format | 3zr9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zr/3zr9 ftp://data.pdbj.org/pub/pdb/validation_reports/zr/3zr9 | HTTPS FTP |
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-Related structure data
Related structure data | 2whgS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 24343.371 Da / Num. of mol.: 1 / Fragment: BETA-LACTAMASE, RESIDUES 42-270 Source method: isolated from a genetically manipulated source Source: (gene. exp.) KLEBSIELLA PNEUMONIAE (bacteria) / Plasmid: POPINF / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ROSETTA PLYSS / References: UniProt: C7C422, beta-lactamase |
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-Non-polymers , 5 types, 123 molecules
#2: Chemical | ChemComp-ZN / | ||||
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#3: Chemical | ChemComp-CO / | ||||
#4: Chemical | ChemComp-NI / #5: Chemical | ChemComp-CD / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.28 Å3/Da / Density % sol: 62.48 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 5 MM COCL2, 5 MM NICL2, 5 MM MGCL2, 5 MM CDCL2, 100 MM HEPES PH 7.5, 12% (W/V) PEG 3350. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9163 |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 14, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9163 Å / Relative weight: 1 |
Reflection | Resolution: 1.91→28.79 Å / Num. obs: 25258 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 13.3 % / Biso Wilson estimate: 64.1 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 26.3 |
Reflection shell | Resolution: 1.91→1.96 Å / Redundancy: 12.2 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 3.3 / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WHG Resolution: 1.91→19.56 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.88 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.113 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.772 Å2
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Refinement step | Cycle: LAST / Resolution: 1.91→19.56 Å
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