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Yorodumi- PDB-5n0i: Crystal structure of NDM-1 in complex with beta-mercaptoethanol -... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5n0i | ||||||
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Title | Crystal structure of NDM-1 in complex with beta-mercaptoethanol - new refinement | ||||||
Components | Metallo-beta-lactamase type 2 | ||||||
Keywords | HYDROLASE / NDM-1 / metallo-beta-lactamase | ||||||
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: 1.47 Å | ||||||
Authors | Raczynska, J.E. / Shabalin, I.G. / Jaskolski, M. / Minor, W. / Wlodawer, A. / King, D.T. / Strynadka, N.C.J. | ||||||
Citation | Journal: Drug Resist. Updat. / Year: 2018 Title: A close look onto structural models and primary ligands of metallo-beta-lactamases. Authors: Raczynska, J.E. / Shabalin, I.G. / Minor, W. / Wlodawer, A. / Jaskolski, M. | ||||||
History |
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Remark 0 | THIS ENTRY 5N0I REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA (R4EXYSF) ...THIS ENTRY 5N0I REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA (R4EXYSF) DETERMINED BY AUTHORS OF THE PDB ENTRY 4EXY: D.T.KING, N.C.J.STRYNADKA ORIGINAL DATA REFERENCE 1 PDB ID: 4EXY AUTH D.T.KING,L.J.WORRALL,R.GRUNINGER,N.C.STRYNADKA TITL NEW DELHI METALLO-BETA-LACTAMASE: STRUCTURAL INSIGHTS INTO TITL 2 BETA-LACTAM RECOGNITION AND INHIBITION REF J.AM.CHEM.SOC. V. 134 11362 2012 REFN ISSN 0002-7863 PMID 22713171 DOI 10.1021/JA303579D |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5n0i.cif.gz | 219.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5n0i.ent.gz | 173.7 KB | Display | PDB format |
PDBx/mmJSON format | 5n0i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n0/5n0i ftp://data.pdbj.org/pub/pdb/validation_reports/n0/5n0i | HTTPS FTP |
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-Related structure data
Related structure data | 5n0hC 5nbkC 5o2eC 5o2fC 5w8wC 6ex7C 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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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 25874.160 Da / Num. of mol.: 2 / 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 BL21 (bacteria) / References: UniProt: C7C422, beta-lactamase |
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-Non-polymers , 6 types, 579 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-CL / | #6: Chemical | ChemComp-PG4 / | #7: 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: 2.58 Å3/Da / Density % sol: 52.3 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 10% w/v PEG8K, 8% w/v ethylene glycol, 0.1M HEPES, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.97949 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Nov 22, 2011 |
Radiation | Monochromator: TEROIDAL FOCUSING MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.47→35.74 Å / Num. obs: 91755 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Rsym value: 0.06 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 1.47→1.55 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 3 / Rsym value: 0.372 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.47→35.74 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.827 / SU ML: 0.03 / Cross valid method: FREE R-VALUE / ESU R: 0.048 / ESU R Free: 0.048 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.599 Å2
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Refinement step | Cycle: 1 / Resolution: 1.47→35.74 Å
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Refine LS restraints |
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