+Open data
-Basic information
Entry | Database: PDB / ID: 5zgf | ||||||
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Title | Crystal structure of NDM-1 Q123G mutant | ||||||
Components | Metallo-beta-lactamase type 2 | ||||||
Keywords | HYDROLASE / NDM-1 / metallo-beta-lactamase / antibiotic resistent / conformational change | ||||||
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: 1.2 Å | ||||||
Authors | Zhang, H. / Hao, Q. | ||||||
Funding support | China, 1items
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Citation | Journal: Antimicrob. Agents Chemother. / Year: 2018 Title: Active-Site Conformational Fluctuations Promote the Enzymatic Activity of NDM-1. Authors: Zhang, H. / Ma, G. / Zhu, Y. / Zeng, L. / Ahmad, A. / Wang, C. / Pang, B. / Fang, H. / Zhao, L. / Hao, Q. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zgf.cif.gz | 110.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zgf.ent.gz | 81.4 KB | Display | PDB format |
PDBx/mmJSON format | 5zgf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5zgf_validation.pdf.gz | 2.3 MB | Display | wwPDB validaton report |
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Full document | 5zgf_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 5zgf_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | 5zgf_validation.cif.gz | 21.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zg/5zgf ftp://data.pdbj.org/pub/pdb/validation_reports/zg/5zgf | HTTPS FTP |
-Related structure data
Related structure data | 5zgeC 5zgiC 5zgpC 5zgqC 5zgrC 5zgtC 5zguC 5zgvC 5zgwC 5zgxC 5zgyC 5zgzC 5zh1C 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
#1: Protein | Mass: 25560.744 Da / Num. of mol.: 1 / Mutation: Q123G 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-OH / | #4: 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: 1.92 Å3/Da / Density % sol: 35.94 % / Mosaicity: 0.748 ° / Mosaicity esd: 0.009 ° |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M Sodium succinate pH7.5, 30% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 6, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.2→50 Å / Num. obs: 59277 / % possible obs: 98.4 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.037 / Rpim(I) all: 0.015 / Rrim(I) all: 0.04 / Χ2: 0.881 / Net I/σ(I): 10.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3Q6X 3q6x Resolution: 1.2→41.66 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.22 / SU ML: 0.029 / SU R Cruickshank DPI: 0.042 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.042 / ESU R Free: 0.045 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 67.61 Å2 / Biso mean: 22.184 Å2 / Biso min: 12.64 Å2
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Refinement step | Cycle: final / Resolution: 1.2→41.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.201→1.232 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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