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Yorodumi- PDB-5zge: Crystal structure of NDM-1 at pH5.5 (Bis-Tris) in complex with hy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5zge | |||||||||
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Title | Crystal structure of NDM-1 at pH5.5 (Bis-Tris) in complex with hydrolyzed ampicillin | |||||||||
Components | Metallo-beta-lactamase type 2 | |||||||||
Keywords | HYDROLASE/ANTIBIOTIC / NDM-1 / metallo-beta-lactamase / antibiotic resistent / conformational change / ANTIBIOTIC / HYDROLASE-ANTIBIOTIC complex | |||||||||
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 Å | |||||||||
Authors | Zhang, H. / Hao, Q. | |||||||||
Funding support | China, 1items
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Citation | ||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zge.cif.gz | 224.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zge.ent.gz | 178.3 KB | Display | PDB format |
PDBx/mmJSON format | 5zge.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5zge_validation.pdf.gz | 4.8 MB | Display | wwPDB validaton report |
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Full document | 5zge_full_validation.pdf.gz | 4.8 MB | Display | |
Data in XML | 5zge_validation.xml.gz | 25.8 KB | Display | |
Data in CIF | 5zge_validation.cif.gz | 39.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zg/5zge ftp://data.pdbj.org/pub/pdb/validation_reports/zg/5zge | HTTPS FTP |
-Related structure data
Related structure data | 5zgfC 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _ / Auth seq-ID: 30 - 270 / Label seq-ID: 2 - 242
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-Components
#1: Protein | Mass: 25631.820 Da / Num. of mol.: 2 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 #2: Chemical | #3: Chemical | ChemComp-ZN / #4: Chemical | #5: 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: 2.03 Å3/Da / Density % sol: 39.27 % / Mosaicity: 0.309 ° / 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, 0.2M Li2SO4, 25% PEG 3350, 20 mg/ml ampicillin |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.82653 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 7, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.82653 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1→50 Å / Num. obs: 223485 / % possible obs: 99.2 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.069 / Χ2: 0.931 / Net I/σ(I): 9.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3Q6X 3q6x Resolution: 1→50 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.981 / SU B: 0.66 / SU ML: 0.015 / SU R Cruickshank DPI: 0.0233 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.023 / ESU R Free: 0.024 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: 104.85 Å2 / Biso mean: 22.698 Å2 / Biso min: 15.29 Å2
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Refinement step | Cycle: final / Resolution: 1→50 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 15524 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05
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LS refinement shell | Resolution: 0.999→1.025 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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