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Yorodumi- PDB-1alq: CIRCULARLY PERMUTED BETA-LACTAMASE FROM STAPHYLOCOCCUS AUREUS PC1 -
+Open data
-Basic information
Entry | Database: PDB / ID: 1alq | ||||||
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Title | CIRCULARLY PERMUTED BETA-LACTAMASE FROM STAPHYLOCOCCUS AUREUS PC1 | ||||||
Components | CP254 BETA-LACTAMASE | ||||||
Keywords | HYDROLASE / CIRCULAR PERMUTED / ANTIBIOTIC RESISTANCE | ||||||
Function / homology | Function and homology information beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / DIFFERENCE FOURIER / Resolution: 1.8 Å | ||||||
Authors | Pieper, U. / Herzberg, O. | ||||||
Citation | Journal: Biochemistry / Year: 1997 Title: Circularly permuted beta-lactamase from Staphylococcus aureus PC1. Authors: Pieper, U. / Hayakawa, K. / Li, Z. / Herzberg, O. #1: Journal: J.Mol.Biol. / Year: 1991 Title: Refined Crystal Structure of Beta-Lactamase from Staphylococcus Aureus Pc1 at 2.0 A Resolution Authors: Herzberg, O. #2: Journal: Science / Year: 1987 Title: Bacterial Resistance to Beta-Lactam Antibiotics: Crystal Structure of Beta-Lactamase from Staphylococcus Aureus Pc1 at 2.5 A Resolution Authors: Herzberg, O. / Moult, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1alq.cif.gz | 69.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1alq.ent.gz | 50 KB | Display | PDB format |
PDBx/mmJSON format | 1alq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1alq_validation.pdf.gz | 385.6 KB | Display | wwPDB validaton report |
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Full document | 1alq_full_validation.pdf.gz | 393.7 KB | Display | |
Data in XML | 1alq_validation.xml.gz | 7.4 KB | Display | |
Data in CIF | 1alq_validation.cif.gz | 11.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/al/1alq ftp://data.pdbj.org/pub/pdb/validation_reports/al/1alq | HTTPS FTP |
-Related structure data
Related structure data | 3blmS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 29646.125 Da / Num. of mol.: 1 Mutation: CIRCULARLY PERMUTED WITH AN EIGHT RESIDUE LINKER INSERTED TO JOIN THE ORIGINAL N- AND C-TERMINI, AND A NEW N-TERMINUS AT RESIDUE 254 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Cell line: 293 / Production host: Escherichia coli (E. coli) / Strain (production host): TG1 / References: UniProt: P00807, beta-lactamase |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-CO3 / |
#4: 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: 2.96 Å3/Da / Density % sol: 57 % Description: RESIDUES 31 - 34, 252 - 256, 288 - 290 AND THE SOLVENT WERE EXCLUDED FROM THE STARTING MODEL. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8 Details: PROTEIN WAS CRYSTALLIZED FROM 70% SATURATED AMMONIUM SULFATE SOLUTION, 0.3M KCL, 100MM NAHCO3 AT PH8.0, 0.5% V/V PEG600 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 300 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Oct 1, 1996 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. obs: 29813 / % possible obs: 89 % / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 20.4 |
Reflection shell | Resolution: 1.8→1.91 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.408 / Mean I/σ(I) obs: 1.8 / % possible all: 66 |
Reflection | *PLUS Num. measured all: 147535 |
-Processing
Software |
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Refinement | Method to determine structure: DIFFERENCE FOURIER Starting model: PDB ENTRY 3BLM Resolution: 1.8→30 Å / Num. parameters: 9029 / Num. restraintsaints: 8373 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH & HUBER Details: INITIAL POSITIONAL AND B-FACTOR REFINEMENT WAS CARRIED OUT WITH X-PLOR (BRUNGER, 1992) FOR DATA IN THE RESOLUTION RANGE 7.0 - 1.9 ANGSTROMS. AT R-VALUES OF R=0.189 AND RFREE=0.241 FOR ...Details: INITIAL POSITIONAL AND B-FACTOR REFINEMENT WAS CARRIED OUT WITH X-PLOR (BRUNGER, 1992) FOR DATA IN THE RESOLUTION RANGE 7.0 - 1.9 ANGSTROMS. AT R-VALUES OF R=0.189 AND RFREE=0.241 FOR I>I/SIGMA(I) THE REFINEMENT WAS CONTINUED WITH THE PROGRAM SHELXL.
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Solvent computation | Solvent model: MOEWS & KRETSINGER | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 2122 / Occupancy sum non hydrogen: 2203.5 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→30 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: s_plane_restr / Dev ideal: 0.034 |