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Yorodumi- PDB-1blh: STRUCTURE OF A PHOSPHONATE-INHIBITED BETA-LACTAMASE. AN ANALOG OF... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1blh | ||||||
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Title | STRUCTURE OF A PHOSPHONATE-INHIBITED BETA-LACTAMASE. AN ANALOG OF THE TETRAHEDRAL TRANSITION STATE(SLASH)INTERMEDIATE OF BETA-LACTAM HYDROLYSIS | ||||||
Components | BETA-LACTAMASE | ||||||
Keywords | HYDROLASE(BETA-LACTAMASE) | ||||||
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 / Resolution: 2.3 Å | ||||||
Authors | Chen, C.C.H. / Herzberg, O. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1993 Title: Structure of a phosphonate-inhibited beta-lactamase. An analog of the tetrahedral transition state/intermediate of beta-lactam hydrolysis. Authors: Chen, C.C. / Rahil, J. / Pratt, R.F. / Herzberg, O. #1: Journal: J.Mol.Biol. / Year: 1992 Title: Inhibition of Beta-Lactamase by Clavulanate. Trapped Intermediates in Cryocrystallographic Studies Authors: Chen, C.C.H. / Herzberg, O. #2: Journal: J.Mol.Biol. / Year: 1991 Title: Refined Crystal Structure of Beta-Lactamase from Staphylococcus Aureus Pc1 at 2.0 Angstroms Resolution Authors: Herzberg, O. #3: Journal: Biochemistry / Year: 1991 Title: Structural Basis for the Inactivation of the P54 Mutant of Beta-Lactamase from Staphylococcus Aureus Pc1 Authors: Herzberg, O. / Kapadia, G. / Blanco, B. / Smith, T.S. / Coulson, A. #4: Journal: Curr.Opin.Struct.Biol. / Year: 1991 Title: Penicillin-Binding and Degrading Enzymes Authors: Herzberg, O. / Moult, J. #5: Journal: Science / Year: 1987 Title: Bacterial Resistance to Beta-Lactam Antibiotics. Crystal Structure of Beta-Lactamase from Staphylococcus Aureus Pc1 at 2.5 Angstroms Resolution Authors: Herzberg, O. / Moult, J. #6: Journal: Biochem.J. / Year: 1985 Title: The Crystal Structure of Beta-Lactamase from Staphylococcus Aureus at 0.5Nm Resolution Authors: Moult, J. / Sawyer, L. / Herzberg, O. / Jones, C.L. / Coulson, A.F.W. / Green, D.W. / Harding, M.M. / Ambler, R.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1blh.cif.gz | 67.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1blh.ent.gz | 48.9 KB | Display | PDB format |
PDBx/mmJSON format | 1blh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bl/1blh ftp://data.pdbj.org/pub/pdb/validation_reports/bl/1blh | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: GLU 166 - ILE 167 OMEGA = 1.57 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION | ||||||||
Components on special symmetry positions |
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-Components
#1: Protein | Mass: 28843.211 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / References: UniProt: P00807, beta-lactamase |
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#2: Chemical | ChemComp-FOS / [[ |
#3: Water | ChemComp-HOH / |
Compound details | THE ACTIVE SITE SERINE IS SER 70. THERE IS AN OXYANION HOLE FORMED BY THE MAIN CHAIN NITROGEN ATOMS ...THE ACTIVE SITE SERINE IS SER 70. THERE IS AN OXYANION HOLE FORMED BY THE MAIN CHAIN NITROGEN ATOMS OF SER 70 AND GLN 237, IN A SIMILAR MANNER TO THE SERINE PROTEASE STRUCTURES |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.06 Å3/Da / Density % sol: 59.8 % | ||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 8 / Method: unknownDetails: referred to 'Herzberg, O.', (1987) Science, 236, 694-701 | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.3 Å / Num. all: 16164 / Num. obs: 14163 / Num. measured all: 46421 / Biso Wilson estimate: 26.4 Å2 |
-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.3→8 Å / Rfactor obs: 0.166 / σ(F): 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→8 Å
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Refine LS restraints |
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Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 11735 / Rfactor obs: 0.166 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |