+Open data
-Basic information
Entry | Database: PDB / ID: 5fq9 | ||||||
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Title | Crystal structure of the OXA10 with 1C | ||||||
Components | BETA-LACTAMASE OXA-10 | ||||||
Keywords | HYDROLASE / ANTIBIOTIC RESISTANCE | ||||||
Function / homology | Function and homology information penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | PSEUDOMONAS AERUGINOSA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Brem, J. / McDonough, M.A. / Cain, R. / Clifton, I. / Fishwick, C.W.G. / Schofield, C.J. | ||||||
Citation | Journal: Nat Commun / Year: 2016 Title: Structural basis of metallo-beta-lactamase, serine-beta-lactamase and penicillin-binding protein inhibition by cyclic boronates. Authors: Brem, J. / Cain, R. / Cahill, S. / McDonough, M.A. / Clifton, I.J. / Jimenez-Castellanos, J.C. / Avison, M.B. / Spencer, J. / Fishwick, C.W. / Schofield, C.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fq9.cif.gz | 220.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fq9.ent.gz | 176.4 KB | Display | PDB format |
PDBx/mmJSON format | 5fq9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fq9_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 5fq9_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 5fq9_validation.xml.gz | 26.5 KB | Display | |
Data in CIF | 5fq9_validation.cif.gz | 38.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fq/5fq9 ftp://data.pdbj.org/pub/pdb/validation_reports/fq/5fq9 | HTTPS FTP |
-Related structure data
Related structure data | 5fqbC 5fqcC 5j8xC 1k6rS C: citing same article (ref.) 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.8054, 0.591, 0.0452), Vector: |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 27755.541 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: 1C BOUND TO THE ACTIVE SITE / Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P14489, beta-lactamase |
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-Non-polymers , 6 types, 500 molecules
#2: Chemical | #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-ACT / | #5: Chemical | ChemComp-CL / | #6: Chemical | ChemComp-NA / | #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: 3.17 Å3/Da / Density % sol: 61.15 % / Description: NONE |
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Crystal grow | pH: 5.5 / Details: 0.2M NACL, 0.1M NA ACETATE PH 5.0, 20% PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 27, 2015 / Details: MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→15.44 Å / Num. obs: 253261 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 5.9 % / Biso Wilson estimate: 16.1 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 5.6 |
Reflection shell | Resolution: 1.1→1.12 Å / Redundancy: 8.9 % / Rmerge(I) obs: 1.1 / Mean I/σ(I) obs: 2 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1K6R Resolution: 1.5→15.424 Å / SU ML: 0.15 / σ(F): 1.34 / Phase error: 17.79 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.325 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→15.424 Å
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Refine LS restraints |
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LS refinement shell |
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