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Yorodumi- PDB-5zj8: Crystal structure of NDM-1 in complex with D-captopril derivative CY32 -
+Open data
-Basic information
Entry | Database: PDB / ID: 5zj8 | ||||||
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Title | Crystal structure of NDM-1 in complex with D-captopril derivative CY32 | ||||||
Components | Metallo-beta-lactamase type 2 | ||||||
Keywords | HYDROLASE / NDM-1 / metallo-beta-lactamase / antibiotic resistent / inhibitor / thio compounds | ||||||
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: 0.96 Å | ||||||
Authors | Zhang, H. / Hao, Q. | ||||||
Funding support | China, 1items
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Citation | Journal: to be published Title: Crystal structure of NDM-1 Authors: Zhang, H. / Hao, Q. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zj8.cif.gz | 116.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zj8.ent.gz | 87.9 KB | Display | PDB format |
PDBx/mmJSON format | 5zj8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zj/5zj8 ftp://data.pdbj.org/pub/pdb/validation_reports/zj/5zj8 | HTTPS FTP |
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-Related structure data
Related structure data | 5zj1C 5zj7C 5zjcC 3q6x C: citing same article (ref.) 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: 25631.820 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaNDM-1 / Plasmid: pRHisMBP / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: C7C422, beta-lactamase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-9DC / ( | #4: Chemical | ChemComp-EDO / #5: 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: 2.01 Å3/Da / Density % sol: 38.95 % / Mosaicity: 0.358 ° / Mosaicity esd: 0.004 ° |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1M Bis-Tris pH5.5, 15% PEG 3350, 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: Sep 22, 2013 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 0.96→50 Å / Num. obs: 119590 / % possible obs: 96.6 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.097 / Χ2: 0.923 / Net I/σ(I): 20.2 / Num. measured all: 702557 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3Q6X 3q6x Resolution: 0.96→41.53 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.985 / WRfactor Rfree: 0.1345 / WRfactor Rwork: 0.1193 / FOM work R set: 0.8634 / SU B: 0.573 / SU ML: 0.013 / SU R Cruickshank DPI: 0.0184 / SU Rfree: 0.0184 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.018 / ESU R Free: 0.018 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 95.77 Å2 / Biso mean: 22.802 Å2 / Biso min: 15.95 Å2
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Refinement step | Cycle: final / Resolution: 0.96→41.53 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 0.96→0.985 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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