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Yorodumi- PDB-7bz3: The mutant variant of PNGM-1. H257 was substituted for alanine to... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7bz3 | ||||||
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Title | The mutant variant of PNGM-1. H257 was substituted for alanine to study substrate binding. | ||||||
Components | Metallo-beta-lactamase PNGM-1 | ||||||
Keywords | ANTIBIOTIC / RNase Z / MBLs / carbapenemase | ||||||
Function / homology | Function and homology information 3'-tRNA processing endoribonuclease activity / beta-lactamase activity / beta-lactamase / metal ion binding Similarity search - Function | ||||||
Biological species | uncultured bacterium (environmental samples) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Model details | PNGM-1 residue H96 was substitued for alanine | ||||||
Authors | Park, Y.S. / Kang, L.W. / Lee, J.H. | ||||||
Citation | Journal: Int J Mol Sci / Year: 2020 Title: Structural Study of Metal Binding and Coordination in Ancient Metallo-beta-Lactamase PNGM-1 Variants. Authors: Park, Y.S. / Kim, T.Y. / Park, H. / Lee, J.H. / Nguyen, D.Q. / Hong, M.K. / Lee, S.H. / Kang, L.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7bz3.cif.gz | 296.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bz3.ent.gz | 237.2 KB | Display | PDB format |
PDBx/mmJSON format | 7bz3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bz/7bz3 ftp://data.pdbj.org/pub/pdb/validation_reports/bz/7bz3 | HTTPS FTP |
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-Related structure data
Related structure data | 7byqC 7bz1C 7bz4C 7bziC 7wi1C C: citing same article (ref.) |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.1107/S2053230X18012268 / Data set type: other data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 41634.457 Da / Num. of mol.: 4 / Mutation: H257A Source method: isolated from a genetically manipulated source Source: (gene. exp.) uncultured bacterium (environmental samples) Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2U8UYM6, beta-lactamase #2: Chemical | ChemComp-ZN / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.55 Å3/Da / Density % sol: 51.76 % / Mosaicity: 0.5 ° |
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Crystal grow | Temperature: 287 K / Method: evaporation / pH: 4.6 Details: 0.1 M Sodium acetate, 20% glycerol, 0.2 M MgCl2 and 7.5% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K Ambient temp details: steady flow of liquid nitrogen was used to maintain 100 K. Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 8, 2013 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→50 Å / Num. obs: 103806 / % possible obs: 97.6 % / Redundancy: 6.2 % / CC1/2: 0.987 / CC star: 0.997 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.039 / Rrim(I) all: 0.097 / Rsym value: 0.089 / Χ2: 3.751 / Net I/av σ(I): 37.603 / Net I/σ(I): 12.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→48.69 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.866 / SU B: 5.999 / SU ML: 0.166 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.211 / ESU R Free: 0.196 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: 118.97 Å2 / Biso mean: 24.755 Å2 / Biso min: 8.8 Å2
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Refinement step | Cycle: final / Resolution: 2→48.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.051 Å / Rfactor Rfree error: 0
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