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Yorodumi- PDB-1z6f: Crystal structure of penicillin-binding protein 5 from E. coli in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1z6f | ||||||
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Title | Crystal structure of penicillin-binding protein 5 from E. coli in complex with a boronic acid inhibitor | ||||||
Components | Penicillin-binding protein 5 | ||||||
Keywords | HYDROLASE / peptidoglycan synthesis / penicillin-binding protein / dd-carboxypeptidase / boronic acid | ||||||
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 / SYNCHROTRON / SIMPLE REFINEMENT / Resolution: 1.6 Å | ||||||
Authors | Nicola, G. / Peddi, S. / Stefanova, M. / Nicholas, R.A. / Gutheil, W.G. / Davies, C. | ||||||
Citation | Journal: Biochemistry / Year: 2005 Title: Crystal Structure of Escherichia coli Penicillin-Binding Protein 5 Bound to a Tripeptide Boronic Acid Inhibitor: A Role for Ser-110 in Deacylation. Authors: Nicola, G. / Peddi, S. / Stefanova, M. / Nicholas, R.A. / Gutheil, W.G. / Davies, C. | ||||||
History |
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Remark 999 | SEQUENCE TO PRODUCE SPBP 5, THE LAST 17 AMINO ACIDS WERE REMOVED BY DELETION OF THEIR RESPECTIVE ...SEQUENCE 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 | 1z6f.cif.gz | 93.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1z6f.ent.gz | 68.7 KB | Display | PDB format |
PDBx/mmJSON format | 1z6f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1z6f_validation.pdf.gz | 701.7 KB | Display | wwPDB validaton report |
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Full document | 1z6f_full_validation.pdf.gz | 706.3 KB | Display | |
Data in XML | 1z6f_validation.xml.gz | 19.3 KB | Display | |
Data in CIF | 1z6f_validation.cif.gz | 29.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z6/1z6f ftp://data.pdbj.org/pub/pdb/validation_reports/z6/1z6f | HTTPS FTP |
-Related structure data
Related structure data | 1nzoS 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, pfv / 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 | ChemComp-BO9 / |
#3: Chemical | ChemComp-GOL / |
#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: 2.9 Å3/Da / Density % sol: 57 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 100mM Tris, 8% PEG 400, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 24, 2004 |
Radiation | Monochromator: Double crystal monochromator Si-220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→30 Å / Num. all: 52064 / Num. obs: 52064 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 21.5 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 24.4 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.466 / Mean I/σ(I) obs: 2.4 / Num. unique all: 5239 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: SIMPLE REFINEMENT Starting model: PDB entry 1NZO Resolution: 1.6→30 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.94 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.101 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.342 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.641 Å / Total num. of bins used: 20
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