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Yorodumi- PDB-1nzo: The crystal structure of wild type penicillin-binding protein 5 f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nzo | ||||||
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Title | The crystal structure of wild type penicillin-binding protein 5 from E. coli | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Nicholas, R.A. / Krings, S. / Tomberg, J. / Nicola, G. / Davies, C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: Crystal structure of wild-type penicillin-binding protein 5 from Escherichia coli: implications for deacylation of the acyl-enzyme complex. Authors: Nicholas, R.A. / Krings, S. / Tomberg, J. / Nicola, G. / Davies, C. #1: 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. | ||||||
History |
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Remark 999 | SEQUENCE THIS IS A SOLUBLE CONSTRUCT OF A MUTANT PBP 5, TERMED SPBP 5 TO PRODUCE SPBP 5, THE LAST ...SEQUENCE THIS IS A SOLUBLE CONSTRUCT OF A MUTANT PBP 5, TERMED SPBP 5 TO PRODUCE SPBP 5, THE LAST 17 AMINO ACIDS WERE REMOVED BY DELETION OF THEIR RESPECTIVE CODONS, AN ADDITIONAL SIX AMINO ACIDS (GDPVID) WERE INTRODUCED AT THE C TERMINUS DUE TO READ-THROUGH TO THE STOP CODON. NONE OF THESE NON-NATIVE RESIDUES ARE VISIBLE IN THE ELECTRON DENSITY MAP. THE FIRST 29 AMINO ACIDS OF THE PROTEIN ENCODED BY THE OPEN READING FRAME REPRESENT THE SIGNAL SEQUENCE, WHICH IS REMOVED DURING MATURATION AND TRANSPORT TO THE PERIPLASMIC SPACE AND IS NOT PRESENT IN THIS CONSTRUCT. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nzo.cif.gz | 85.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nzo.ent.gz | 63.6 KB | Display | PDB format |
PDBx/mmJSON format | 1nzo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nzo_validation.pdf.gz | 440 KB | Display | wwPDB validaton report |
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Full document | 1nzo_full_validation.pdf.gz | 446.8 KB | Display | |
Data in XML | 1nzo_validation.xml.gz | 17.3 KB | Display | |
Data in CIF | 1nzo_validation.cif.gz | 24.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nz/1nzo ftp://data.pdbj.org/pub/pdb/validation_reports/nz/1nzo | HTTPS FTP |
-Related structure data
Related structure data | 1nj4C 1hd8S 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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-Components
#1: Protein | Mass: 39841.117 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: DACA / Plasmid: PBR322 / 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: Chemical | #3: 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: 2.5 Å3/Da / Density % sol: 50.83 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 100mM Tris pH 7.0, 8% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 10, 2002 / Details: mirrors |
Radiation | Monochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→54 Å / Num. all: 31624 / Num. obs: 31624 / % possible obs: 93.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 29.4 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 4 % / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 2 / Num. unique all: 2269 / % possible all: 67.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HD8 Resolution: 1.85→14.92 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.933 / SU B: 4.3 / SU ML: 0.126 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.163 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.949 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→14.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.897 Å / Total num. of bins used: 20
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