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Yorodumi- PDB-5xhr: Crystal structure of P99 beta-lactamase in complex with a penicil... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xhr | ||||||
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Title | Crystal structure of P99 beta-lactamase in complex with a penicillin derivative MPC-1 | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic Similarity search - Function | ||||||
Biological species | Enterobacter cloacae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Pan, X. / Zhao, Y. | ||||||
Citation | Journal: Antimicrob. Agents Chemother. / Year: 2017 Title: Modified Penicillin Molecule with Carbapenem-Like Stereochemistry Specifically Inhibits Class C beta-Lactamases Authors: Pan, X. / He, Y. / Chen, T. / Chan, K.F. / Zhao, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xhr.cif.gz | 88.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xhr.ent.gz | 64.7 KB | Display | PDB format |
PDBx/mmJSON format | 5xhr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5xhr_validation.pdf.gz | 739.1 KB | Display | wwPDB validaton report |
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Full document | 5xhr_full_validation.pdf.gz | 743.7 KB | Display | |
Data in XML | 5xhr_validation.xml.gz | 16.6 KB | Display | |
Data in CIF | 5xhr_validation.cif.gz | 23.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xh/5xhr ftp://data.pdbj.org/pub/pdb/validation_reports/xh/5xhr | HTTPS FTP |
-Related structure data
Related structure data | 1xx2S S: Starting model for refinement |
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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: 39568.055 Da / Num. of mol.: 1 / Fragment: UNP residues 21-381 Source method: isolated from a genetically manipulated source Details: PNM / Source: (gene. exp.) Enterobacter cloacae (bacteria) / Gene: ampC / Production host: Escherichia coli (E. coli) / References: UniProt: P05364, beta-lactamase |
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#2: Chemical | ChemComp-PXH / ( |
#3: 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: 2.06 Å3/Da / Density % sol: 40.26 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / Details: 0.1M Bis-Tris pH 6.5, 25% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.91836 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 13, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91836 Å / Relative weight: 1 |
Reflection | Resolution: 1.74→69.33 Å / Num. obs: 30924 / % possible obs: 99.4 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.292 / Mean I/σ(I) obs: 6.2 / Rsym value: 0.292 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1XX2 Resolution: 1.8→69 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.904 / SU B: 3.116 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.136 / 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: 11.994 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→69 Å
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Refine LS restraints |
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