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Yorodumi- PDB-2jch: Structural and mechanistic basis of penicillin binding protein in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2jch | ||||||
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Title | Structural and mechanistic basis of penicillin binding protein inhibition by lactivicins | ||||||
Components | PENICILLIN-BINDING PROTEIN 1B | ||||||
Keywords | DRUG-BINDING PROTEIN / PEPTIDOGLYCAN SYNTHESIS MULTIFUNCTIONAL ENZYME / CELL WALL / PEPTIDOGLYCAN / GAMMA LACTAM ANTIBIOTICS / BINDING PROTEIN | ||||||
Function / homology | Function and homology information peptidoglycan glycosyltransferase / peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / proteolysis / extracellular region / membrane Similarity search - Function | ||||||
Biological species | STREPTOCOCCUS PNEUMONIAE (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Macheboeuf, P. / Fisher, D.S. / Brown, T.J. / Zervosen, A. / Luxen, A. / Joris, B. / Dessen, A. / Schofield, C.J. | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2007 Title: Structural and Mechanistic Basis of Penicillin-Binding Protein Inhibition by Lactivicins Authors: Macheboeuf, P. / Fisher, D.S. / Brown, T.J. / Zervosen, A. / Luxen, A. / Joris, B. / Dessen, A. / Schofield, C.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2jch.cif.gz | 113.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jch.ent.gz | 83.4 KB | Display | PDB format |
PDBx/mmJSON format | 2jch.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jc/2jch ftp://data.pdbj.org/pub/pdb/validation_reports/jc/2jch | HTTPS FTP |
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-Related structure data
Related structure data | 2je5C 2bg1S 2bg4 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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 78428.328 Da / Num. of mol.: 1 / Fragment: RESIDUES 72-791 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Strain: R6 / Plasmid: PGEX4T1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O70038 |
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-Non-polymers , 5 types, 151 molecules
#2: Chemical | ChemComp-SO4 / |
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#3: Chemical | ChemComp-CL / |
#4: Chemical | ChemComp-EDO / |
#5: Chemical | ChemComp-PL7 / ( |
#6: Water | ChemComp-HOH / |
-Details
Compound details | ENGINEERED RESIDUE IN CHAIN A, ALA 73 TO SER ENGINEERED RESIDUE IN CHAIN A, LEU 123 TO MET ...ENGINEERED |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.5 Å3/Da / Density % sol: 67.7 % / Description: NONE |
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Crystal grow | pH: 7 / Details: 50 MM HEPES PH 7 3.2 M NACL 0.8 M AMMONIUM SULFATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 12, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→19.9 Å / Num. obs: 29294 / % possible obs: 99.3 % / Observed criterion σ(I): 3 / Redundancy: 5.2 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 2.4→2.6 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.9 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2BG1 Resolution: 2.4→85.13 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.893 / SU B: 7.898 / SU ML: 0.187 / Cross valid method: THROUGHOUT / ESU R: 0.268 / ESU R Free: 0.235 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.7 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→85.13 Å
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Refine LS restraints |
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