+Open data
-Basic information
Entry | Database: PDB / ID: 1k56 | ||||||
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Title | OXA 10 class D beta-lactamase at pH 6.5 | ||||||
Components | (OXA10 beta-lactamase) x 2 | ||||||
Keywords | HYDROLASE / beta-lactamase / antibiotic resistance / carbamylation | ||||||
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 / FOURIER SYNTHESIS / Resolution: 1.7 Å | ||||||
Authors | Golemi, D. / Maveyraud, L. / Vakulenko, S. / Samama, J.P. / Mobashery, S. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2001 Title: Critical involvement of a carbamylated lysine in catalytic function of class D beta-lactamases. Authors: Golemi, D. / Maveyraud, L. / Vakulenko, S. / Samama, J.P. / Mobashery, S. #1: Journal: Structure / Year: 2000 Title: Insights into class D beta-lactamases are revealed by the crystal structure of the OXA10 enzyme from Pseudomonas aeruginosa Authors: Maveyraud, L. / Golemi, D. / Kotra, L.P. / Tranier, S. / Vakulenko, S. / Mobashery, S. / Samama, J.P. #2: Journal: J.Am.Chem.Soc. / Year: 2000 Title: The first structural and mechanistic insights for class D beta-lactamases: evidence for a novel catalytic process for turnover of beta-lactam antibiotic Authors: Golemi, D. / Maveyraud, L. / Vakulenko, S. / Tranier, S. / Ishiwata, A. / Kotra, L.P. / Samama, J.P. / Mobashery, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1k56.cif.gz | 401.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k56.ent.gz | 327.5 KB | Display | PDB format |
PDBx/mmJSON format | 1k56.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k5/1k56 ftp://data.pdbj.org/pub/pdb/validation_reports/k5/1k56 | HTTPS FTP |
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-Related structure data
Related structure data | 1k54C 1k55C 1k57C 1e4dS S: Starting model for refinement C: citing same article (ref.) |
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Similar 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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Details | the biological assembly is a dimer. There are two dimers in the asymmetric unit : chains A and C form a dimer chains B and D form a dimer |
-Components
#1: Protein | Mass: 27567.293 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: Residue 70 of chains A and B are KCX are carbamylated lysine. Residue 70 of chain C exists in two alternate conformations: KCX, carbamylated lysine, and lysine. Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: P14489, beta-lactamase #2: Protein | | Mass: 27524.291 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Residue 70, LYS, is non-carbamylated. / Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: P14489, beta-lactamase #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | Sequence details | RESIDUE 70 OF CHAINS A AND B ARE KCX, CARBAMYLATED LYSINE. RESIDUE 70 OF CHAIN C EXISTS IN TWO ...RESIDUE 70 OF CHAINS A AND B ARE KCX, CARBAMYLAT | |
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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: 2.52 Å3/Da / Density % sol: 51.24 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: ammonium sulphate, HEPES. Crystallization occured at pH 7.5. After obtaining the crystal, the pH was lowered to 6.5 for data collection., VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.8 | ||||||||||||||||||||||||||||||
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: ID14-1 / Wavelength: 0.934 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 4, 2001 |
Radiation | Monochromator: Germanium Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→27.4 Å / Num. all: 118305 / Num. obs: 118305 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 20.383 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.341 / Mean I/σ(I) obs: 4.1 / Num. unique all: 17487 / Rsym value: 0.341 / % possible all: 99.7 |
Reflection | *PLUS Num. measured all: 307069 |
Reflection shell | *PLUS % possible obs: 99.7 % / Num. unique obs: 17487 / Num. measured obs: 44375 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 1E4D Resolution: 1.7→27 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: engh & huber Details: In chains A and B, residue 70 is KCX, a carbamylated lysine (LYSINE NZ-CARBOXYLIC ACID). In chain C, residue 70 exists in two conformations: conformation A, as KCX, and conformation B, as ...Details: In chains A and B, residue 70 is KCX, a carbamylated lysine (LYSINE NZ-CARBOXYLIC ACID). In chain C, residue 70 exists in two conformations: conformation A, as KCX, and conformation B, as LYS. In chain D, residue 70 is a lysine. Water molecule 240 is associated with conformation B of Lys70C.
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Displacement parameters | Biso mean: 16.621 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→27 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 27 Å / σ(F): 0 / % reflection Rfree: 2 % / Rfactor obs: 0.18344 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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