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Yorodumi- PDB-4mut: Crystal structure of vancomycin resistance D,D-dipeptidase/D,D-pe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4mut | ||||||
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Title | Crystal structure of vancomycin resistance D,D-dipeptidase/D,D-pentapeptidase VanXYc D59S mutant in complex with D-Alanine | ||||||
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 D / D-DIPEPTIDASE / D-PENTAPEPTIDASE / VANCOMYCIN RESISTANCE / ANTIBIOTIC RESISTANCE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Enterococcus gallinarum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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 | 4mut.cif.gz | 184.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mut.ent.gz | 144.7 KB | Display | PDB format |
PDBx/mmJSON format | 4mut.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4mut_validation.pdf.gz | 475.3 KB | Display | wwPDB validaton report |
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Full document | 4mut_full_validation.pdf.gz | 478.5 KB | Display | |
Data in XML | 4mut_validation.xml.gz | 20.3 KB | Display | |
Data in CIF | 4mut_validation.cif.gz | 29 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mu/4mut ftp://data.pdbj.org/pub/pdb/validation_reports/mu/4mut | HTTPS FTP |
-Related structure data
Related structure data | 4f78SC 4muqC 4murC 4musC 4oakC 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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2 |
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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 , 6 types, 322 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CL / | #5: Chemical | ChemComp-PE3 / | #6: Chemical | ChemComp-SO4 / | #7: 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: 2.25 Å3/Da / Density % sol: 45.27 % |
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Crystal grow | Temperature: 273 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.1 M magnesium chloride, 0.05 M MES, 20% PEG 8K, 2.5 mM acetyl-L-Lys-D-Ala-D-Ala, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 273K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Feb 17, 2013 / Details: C(111) |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→39.13 Å / Num. obs: 20150 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 2.25→2.37 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.573 / Mean I/σ(I) obs: 2.4 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 4F78 Resolution: 2.25→34.567 Å / SU ML: 0.24 / σ(F): 1.96 / Phase error: 20.78 / 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: 2.25→34.567 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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