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Yorodumi- PDB-1nj4: Crystal structure of a deacylation-defective mutant of penicillin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nj4 | ||||||
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Title | Crystal structure of a deacylation-defective mutant of penicillin-binding protein 5 at 1.9 A resolution | ||||||
Components | Penicillin-binding protein 5 | ||||||
Keywords | HYDROLASE / peptidoglycan synthesis / penicllin-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 / Refinement from a lower resolution structure / Resolution: 1.9 Å | ||||||
Authors | Nicola, G. / Nicholas, R.A. / 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 penicllin-binding protein at 2.3 A resolution Authors: Davies, C. / White, S.W. / Nicholas, R.A. #2: Journal: Rev.Infect.Dis. / Year: 1988 Title: Relations between beta-lactamases and penicllin-binding proteins: beta-lactamase activity of penicillin-binding protein 5 from Escherichia coli Authors: Nicholas, R.A. / Strominger, J.L. #3: 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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Remark 999 | SEQUENCE This is a soluble construct of a mutant PBP 5, termed sPBP 5'. To produce sPBP5', codons ...SEQUENCE This is a soluble construct of a mutant PBP 5, termed sPBP 5'. To produce sPBP5', codons corresponding to the last 17 amino acid residues were removed but an additional six amino acids (GDPVID) were added 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. These residues are not present in this construct. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nj4.cif.gz | 84.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nj4.ent.gz | 62.5 KB | Display | PDB format |
PDBx/mmJSON format | 1nj4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nj4_validation.pdf.gz | 430.8 KB | Display | wwPDB validaton report |
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Full document | 1nj4_full_validation.pdf.gz | 440.1 KB | Display | |
Data in XML | 1nj4_validation.xml.gz | 17.1 KB | Display | |
Data in CIF | 1nj4_validation.cif.gz | 24.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nj/1nj4 ftp://data.pdbj.org/pub/pdb/validation_reports/nj/1nj4 | HTTPS FTP |
-Related structure data
Related structure data | 1nzoC 1hd8S 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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Unit cell |
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-Components
#1: Protein | Mass: 39899.152 Da / Num. of mol.: 1 / Mutation: G105D Source method: isolated from a genetically manipulated source Details: This mutant form of PBP 5 is termed sPBP 5' / 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: 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: 2.48 Å3/Da / Density % sol: 50.31 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 20% PEG 4000, 100 mM Tris pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-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: Oct 8, 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: 1.9→36.6 Å / Num. obs: 29772 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 25.9 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 1.8 / Num. unique all: 3024 / % possible all: 88.4 |
Reflection | *PLUS Num. measured all: 178730 |
Reflection shell | *PLUS % possible obs: 88.4 % / Rmerge(I) obs: 0.358 |
-Processing
Software |
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Refinement | Method to determine structure: Refinement from a lower resolution structure Starting model: PDB ENTRY 1HD8 Resolution: 1.9→15 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.413 / SU ML: 0.127 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.166 / ESU R Free: 0.151 / 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: 29.263 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20 /
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Refinement | *PLUS Lowest resolution: 15 Å / Rfactor obs: 0.209 / Rfactor Rfree: 0.244 / Rfactor Rwork: 0.207 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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