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Yorodumi- PDB-2ex8: Crystal structure of penicillin binding protein 4 (dacB) from Esc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ex8 | ||||||
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Title | Crystal structure of penicillin binding protein 4 (dacB) from Escherichia coli, complexed with penicillin-G | ||||||
Components | Penicillin-binding protein 4 | ||||||
Keywords | HYDROLASE / penicillin-binding protein / penicillin-G / cephem / penem / D-alanyl-D-alanine-carboxypeptidase / D-alanyl-D-alanine-endopeptidase | ||||||
Function / homology | Function and homology information serine-type carboxypeptidase activity / peptidoglycan metabolic process / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / peptidoglycan biosynthetic process / carboxypeptidase activity / cell wall organization / regulation of cell shape ...serine-type carboxypeptidase activity / peptidoglycan metabolic process / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / peptidoglycan biosynthetic process / carboxypeptidase activity / cell wall organization / regulation of cell shape / endopeptidase activity / periplasmic space / cell cycle / cell division / response to antibiotic / serine-type endopeptidase activity / proteolysis / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Kishida, H. / Unzai, S. / Roper, D.I. / Lloyd, A. / Park, S.-Y. / Tame, J.R.H. | ||||||
Citation | Journal: Biochemistry / Year: 2006 Title: Crystal structure of penicillin binding protein 4 (dacB) from Escherichia coli, both in the native form and covalently linked to various antibiotics Authors: Kishida, H. / Unzai, S. / Roper, D.I. / Lloyd, A. / Park, S.-Y. / Tame, J.R.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ex8.cif.gz | 103.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ex8.ent.gz | 82.9 KB | Display | PDB format |
PDBx/mmJSON format | 2ex8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ex/2ex8 ftp://data.pdbj.org/pub/pdb/validation_reports/ex/2ex8 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 49796.711 Da / Num. of mol.: 1 / Mutation: D261Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: DH5 alpha / Gene: dacB / Plasmid: pET21b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P24228, serine-type D-Ala-D-Ala carboxypeptidase, EC: 3.4.99.- |
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#2: Chemical | ChemComp-PNM / |
#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: 2.68 Å3/Da / Density % sol: 54.08 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 5% PEG 20000, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 19, 2005 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 68046 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 19.1 |
Reflection shell | Resolution: 1.6→1.66 Å / Rmerge(I) obs: 0.361 / % possible all: 76.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→20 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.863 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.091 / ESU R Free: 0.091 / 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: 30.168 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→20 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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