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Yorodumi- PDB-4oak: Crystal structure of vancomycin resistance D,D-dipeptidase/D,D-pe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4oak | ||||||
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Title | Crystal structure of vancomycin resistance D,D-dipeptidase/D,D-pentapeptidase VanXYc D59S mutant in complex with D-Alanine-D-Alanine and copper (II) | ||||||
Components | D,D-dipeptidase/D,D-carboxypeptidase | ||||||
Keywords | HYDROLASE / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / CSGID / NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES / NIAID / ALPHA+BETA PROTEIN / METALLOPEPTIDASE / HEDGEHOG/DD-PEPTIDASE FOLD / MEROPS M15B SUBFAMILY / ZN2+-DEPENDENT / VANCOMYCIN RESISTANCE / ANTIBIOTIC RESISTANCE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Enterococcus gallinarum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Stogios, P.J. / Evdokimova, E. / Meziane-Cherif, D. / Di Leo, R. / Yim, V. / Courvalin, P. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2014 Title: Structural basis for the evolution of vancomycin resistance D,D-peptidases. Authors: Meziane-Cherif, D. / Stogios, P.J. / Evdokimova, E. / Savchenko, A. / Courvalin, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4oak.cif.gz | 187.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4oak.ent.gz | 146.6 KB | Display | PDB format |
PDBx/mmJSON format | 4oak.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4oak_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4oak_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4oak_validation.xml.gz | 20.9 KB | Display | |
Data in CIF | 4oak_validation.cif.gz | 29.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oa/4oak ftp://data.pdbj.org/pub/pdb/validation_reports/oa/4oak | HTTPS FTP |
-Related structure data
Related structure data | 4f78C 4muqC 4murSC 4musC 4mutC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 24765.953 Da / Num. of mol.: 2 / Fragment: VanXYc / Mutation: D59S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus gallinarum (bacteria) / Strain: BM4174 / Gene: vanXYc / Plasmid: P15TV-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9JN36 |
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-Non-polymers , 7 types, 344 molecules
#2: Chemical | #3: Chemical | ChemComp-DAL / #4: Chemical | #5: Chemical | ChemComp-MG / | #6: Chemical | ChemComp-CL / #7: Chemical | ChemComp-PE3 / #8: Water | ChemComp-HOH / | |
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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: 2.09 Å3/Da / Density % sol: 41.22 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.1 M MgCl2, 0.05 M MES, 20% PEG8K and 0.1 M phenantroline, 2 h incubation, transferred crystal to new drop with 0.1 M MgCl2, 0.05 M MES, 22% PEG8K and 1 mM CuCl2, 1.5 h incubation, ...Details: 0.1 M MgCl2, 0.05 M MES, 20% PEG8K and 0.1 M phenantroline, 2 h incubation, transferred crystal to new drop with 0.1 M MgCl2, 0.05 M MES, 22% PEG8K and 1 mM CuCl2, 1.5 h incubation, transferred crystal to new drop with 0.1 M MgCl2, 0.05 M MES, 22% PEG8K, 1 mM CuCl2 and 20 mM D-Ala-D-Ala. Cryoprotectant: paratone, pH 5.6, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 12, 2013 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→19.33 Å / Num. obs: 25760 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.518 / Mean I/σ(I) obs: 2.3 / % possible all: 92.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 4MUR Resolution: 2→19.33 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 25.6 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→19.33 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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