+Open data
-Basic information
Entry | Database: PDB / ID: 1h8z | ||||||
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Title | Crystal structure of the class D beta-lactamase OXA-13 | ||||||
Components | BETA-LACTAMASE | ||||||
Keywords | HYDROLASE / BETA-LACTAMASE / CLASS D / OXACILLINASE / OXA-13 | ||||||
Function / homology | Function and homology information penicillin binding / antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | PSEUDOMONAS AERUGINOSA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Pernot, L. / Frenois, F. / Rybkine, T. / L'Hermite, G. / Petrella, S. / Delettre, J. / Jarlier, V. / Collatz, E. / Sougakoff, W. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 Title: Crystal Structures of the Class D B-Lactamase Oxa-13 in the Native Form and in Complex with Meropenem Authors: Pernot, L. / Frenois, F. / Rybkine, T. / L'Hermite, G. / Petrella, S. / Delettre, J. / Jarlier, V. / Collatz, E. / Sougakoff, W. #1: Journal: Microbiology / Year: 1998 Title: Carbapenems as Inhibitors of Oxa-13, a Novel, Integron-Encoded B-Lactamase in Pseudomonas Aeruginosa Authors: Mugnier, P. / Podglajen, I. / Goldstein, F.W. / Collatz, E. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1h8z.cif.gz | 109.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1h8z.ent.gz | 83.5 KB | Display | PDB format |
PDBx/mmJSON format | 1h8z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h8/1h8z ftp://data.pdbj.org/pub/pdb/validation_reports/h8/1h8z | HTTPS FTP |
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-Related structure data
Related structure data | 1h8yC 1ewzS 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: (-0.999894, 0.012941, -0.006663), Vector: |
-Components
#1: Protein | Mass: 27450.260 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAE391 / Gene: BLA OXA-13 / Plasmid: PAZ304 / Gene (production host): BLA OXA-13 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): HB101 / References: UniProt: Q51400, beta-lactamase #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | Sequence details | THE FIRST NINETEEN RESIDUES (MET1-ALA19) DESCRIBED IN THE SEQUENCE DEPOSITED IN THE DATABASE TREMBL ...THE FIRST NINETEEN RESIDUES (MET1-ALA19) DESCRIBED IN THE SEQUENCE DEPOSITED IN THE DATABASE TREMBL ARE NOT PRESENT IN THE MATURE PROTEIN | |
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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: 2.3 Å3/Da / Density % sol: 47 % | |||||||||||||||||||||||||
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Crystal grow | pH: 5.5 Details: 15-17% (W/V) PEG 4000, 0.1M SODIUM CACODYLATE PH 5.0-5.5, 0.2M LITHIUM SULFATE, PROTEIN 12-15 MG/ML | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 13, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. obs: 47483 / % possible obs: 97.3 % / Observed criterion σ(I): 2.5 / Redundancy: 3.5 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 3 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 2.8 / % possible all: 92.8 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 167073 / Rmerge(I) obs: 0.05 |
Reflection shell | *PLUS % possible obs: 92.8 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EWZ Resolution: 1.8→20 Å / SU B: 2.85 / SU ML: 0.09 / σ(F): 0 / ESU R: 0.14 / ESU R Free: 0.14 Details: SEVERAL RESIDUES ARE NOT SEEN IN THE CRYSTAL STRUCTURE, DUE TO DISORDER. THESE INCLUDE THE LOOP FROM ASP A 93 - GLN A 101 AND THE LOOP FROM ASP B 93 - GLN B 101 THE SIDE-CHAIN OF RESIDUE LYS ...Details: SEVERAL RESIDUES ARE NOT SEEN IN THE CRYSTAL STRUCTURE, DUE TO DISORDER. THESE INCLUDE THE LOOP FROM ASP A 93 - GLN A 101 AND THE LOOP FROM ASP B 93 - GLN B 101 THE SIDE-CHAIN OF RESIDUE LYS A 182 HAS ALTERNATE CONFORMATIONS THE SIDE-CHAIN OF THE FOLLOWING RESIDUES HAS BEEN MODELLED A 92, GLU A 103, ARG A 104, LYS B 91, TRP B 92, GLU B 103, ARG B 104.
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Displacement parameters | Biso mean: 29.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.197 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |