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Yorodumi- PDB-1hd8: Crystal structure of a deacylation-defective mutant of penicillin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hd8 | ||||||
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Title | Crystal structure of a deacylation-defective mutant of penicillin-binding protein 5 at 2.3 A resolution | ||||||
Components | PENICILLIN-BINDING PROTEIN 5 | ||||||
Keywords | HYDROLASE / PEPTIDOGLYCAN SYNTHESIS / PENICILLIN-BINDING PROTEIN / DD-CARBOXYPEPTIDASE | ||||||
Function / homology | Function and homology information peptidoglycan metabolic process / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / peptidoglycan biosynthetic process / carboxypeptidase activity / cell wall organization / beta-lactamase activity / beta-lactamase / regulation of cell shape ...peptidoglycan metabolic process / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / peptidoglycan biosynthetic process / carboxypeptidase activity / cell wall organization / beta-lactamase activity / beta-lactamase / regulation of cell shape / outer membrane-bounded periplasmic space / protein homodimerization activity / proteolysis / plasma membrane Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 2.3 Å | ||||||
Authors | Davies, C. / White, S.W. / Nicholas, R.A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2001 Title: Crystal Structure of a Deacylation-Defective Mutant of Penicillin-Binding Protein 5 at 2.3-A Resolution Authors: Davies, C. / White, S.W. / Nicholas, R.A. #1: Journal: Rev.Infect.Dis. / Year: 1988 Title: Relations between Beta-Lactamases and Penicillin-Binding Proteins: Beta-Lactamase Activity of Penicillin-Binding Protein 5 from Escherichia Coli Authors: Nicholas, R.A. / Strominger, J.L. #2: Journal: FEBS Lett. / Year: 1984 Title: An Amino Acid Substitution that Blocks the Deacylation Step in the Enzyme Mechanism of Penicillin-Binding Protein 5 of Escherichia Coli Authors: Broome-Smith, J. / Spratt, B.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hd8.cif.gz | 81 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hd8.ent.gz | 60.7 KB | Display | PDB format |
PDBx/mmJSON format | 1hd8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1hd8_validation.pdf.gz | 369.8 KB | Display | wwPDB validaton report |
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Full document | 1hd8_full_validation.pdf.gz | 385.1 KB | Display | |
Data in XML | 1hd8_validation.xml.gz | 10.1 KB | Display | |
Data in CIF | 1hd8_validation.cif.gz | 15.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hd/1hd8 ftp://data.pdbj.org/pub/pdb/validation_reports/hd/1hd8 | HTTPS FTP |
-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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-Components
#1: Protein | Mass: 39899.152 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Cellular location: PERIPLASM / Gene: DACA / Plasmid: PBR322 / Gene (production host): DACA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): MC1061 References: UniProt: P04287, UniProt: P0AEB2*PLUS, serine-type D-Ala-D-Ala carboxypeptidase |
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#2: Water | ChemComp-HOH / |
Compound details | CHAIN A ENGINEERED MUTATION GLY105ASP TO PRODUCE SPBP 5', THE LAST 17 AMINO ACIDS WERE REMOVED BY ...CHAIN A ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.06 Å3/Da / Density % sol: 59.5 % | ||||||||||||||||||||||||
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Crystal grow | pH: 7 Details: 20% POLYETHYLENE GLYCOL 4000, 50 MM TRIS PH 7.0, 0.2 % SODIUM AZIDE | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / Method: vapor diffusion | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: NONIUS FR391 / Wavelength: 1.5418 |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: Dec 15, 1998 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→22.4 Å / Num. obs: 17239 / % possible obs: 94.8 % / Redundancy: 2.52 % / Biso Wilson estimate: 28.41 Å2 / Rsym value: 0.069 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 3.3 / Rsym value: 0.294 / % possible all: 85.2 |
Reflection | *PLUS Num. measured all: 43406 / Rmerge(I) obs: 0.069 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.3→15 Å / SU B: 8.6 / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.372 / ESU R Free: 0.284 / Details: XPLOR USED IN EARLY STAGES OF REFINEMENT
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Displacement parameters | Biso mean: 35.44 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→15 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 17208 / Rfactor all: 0.207 / Rfactor obs: 0.196 / Rfactor Rfree: 0.27 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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