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Yorodumi- PDB-5ghy: Crystal structure of beta-lactamase PenP mutant-E166H in complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ghy | ||||||
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Title | Crystal structure of beta-lactamase PenP mutant-E166H in complex with cephaloridine as "post-acylation" intermediate | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic / plasma membrane Similarity search - Function | ||||||
Biological species | Bacillus licheniformis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.1 Å | ||||||
Authors | Pan, X. / Zhao, Y. | ||||||
Citation | Journal: J. Biol. Chem. / Year: 2017 Title: Crystallographic Snapshots of Class A beta-Lactamase Catalysis Reveal Structural Changes That Facilitate beta-Lactam Hydrolysis Authors: Pan, X. / He, Y. / Lei, J. / Huang, X. / Zhao, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ghy.cif.gz | 113.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ghy.ent.gz | 91.8 KB | Display | PDB format |
PDBx/mmJSON format | 5ghy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ghy_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 5ghy_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 5ghy_validation.xml.gz | 22.5 KB | Display | |
Data in CIF | 5ghy_validation.cif.gz | 31.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gh/5ghy ftp://data.pdbj.org/pub/pdb/validation_reports/gh/5ghy | HTTPS FTP |
-Related 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
#1: Protein | Mass: 29836.832 Da / Num. of mol.: 2 / Fragment: UNP residues 43-307 / Mutation: E166H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus licheniformis (bacteria) / Gene: penP, blaP / Production host: Escherichia coli (E. coli) / References: UniProt: P00808, beta-lactamase #2: Chemical | #3: 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: 1.96 Å3/Da / Density % sol: 37.36 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop Details: 0.1M Tris pH 8.0, 22.5% PEG 3350, 0.4M ammonium acetate |
-Data collection
Diffraction | Mean temperature: 110 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 7, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.005→63.155 Å / Num. all: 28415 / Num. obs: 28415 / % possible obs: 93.3 % / Redundancy: 3.9 % / Rpim(I) all: 0.04 / Rrim(I) all: 0.079 / Rsym value: 0.068 / Net I/av σ(I): 9.1 / Net I/σ(I): 14.2 / Num. measured all: 111449 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 3.9 %
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-Processing
Software |
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Refinement | Resolution: 2.1→38 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.9 / SU B: 5.872 / SU ML: 0.159 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.347 / ESU R Free: 0.223 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 81.69 Å2 / Biso mean: 21.174 Å2 / Biso min: 8.92 Å2
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Refinement step | Cycle: final / Resolution: 2.1→38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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