+Open data
-Basic information
Entry | Database: PDB / ID: 5xp6 | ||||||
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Title | native structure of NDM-1 crystallized at pH5.5 | ||||||
Components | Metallo-beta-lactamase type 2 | ||||||
Keywords | HYDROLASE / antibiotic resistant / metallo-beta-lactamase / native structure | ||||||
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 / molecular replacement / Resolution: 0.95 Å | ||||||
Authors | Zhang, H. / Ma, G. / Lai, J. / Sun, H. | ||||||
Citation | Journal: Nat Commun / Year: 2018 Title: Bismuth antimicrobial drugs serve as broad-spectrum metallo-beta-lactamase inhibitors Authors: Wang, R. / Lai, T.P. / Gao, P. / Zhang, H. / Ho, P.L. / Woo, P.C. / Ma, G. / Kao, R.Y. / Li, H. / Sun, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xp6.cif.gz | 120.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xp6.ent.gz | 89.8 KB | Display | PDB format |
PDBx/mmJSON format | 5xp6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xp/5xp6 ftp://data.pdbj.org/pub/pdb/validation_reports/xp/5xp6 | HTTPS FTP |
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-Related structure data
Related structure data | 5xp9C 3q6x S: Starting model for refinement C: citing same article (ref.) |
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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: 25718.900 Da / Num. of mol.: 1 / Fragment: UNP residues 29-270 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaNDM-1 Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others) References: UniProt: C7C422, beta-lactamase |
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-Non-polymers , 5 types, 339 molecules
#2: Chemical | #3: Chemical | ChemComp-OH / | #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-SIN / | #6: 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: 2.02 Å3/Da / Density % sol: 38.98 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1M Succinic acid at pH 5.5, 15%(w/v) PEG3350 and 20mM L-proline |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 27, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 0.95→50 Å / Num. obs: 127274 / % possible obs: 99.5 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.094 / Χ2: 1.044 / Net I/σ(I): 12.3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3Q6X 3q6x Resolution: 0.95→41.71 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.976 / SU B: 0.349 / SU ML: 0.009 / SU R Cruickshank DPI: 0.0179 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.018 / ESU R Free: 0.018 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 44.29 Å2 / Biso mean: 8.969 Å2 / Biso min: 4 Å2
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Refinement step | Cycle: final / Resolution: 0.95→41.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 0.95→0.975 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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