+Open data
-Basic information
Entry | Database: PDB / ID: 6h31 | ||||||
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Title | Staphylopine dehydrogenase in the apo state | ||||||
Components | DUF2338 domain-containing protein | ||||||
Keywords | BIOSYNTHETIC PROTEIN / staphylopine biosynthesis | ||||||
Function / homology | staphylopine dehydrogenase / Opine metallophore dehydrogenase / Staphylopine dehydrogenase / oxidoreductase activity / Staphylopine synthase / : Function and homology information | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Hajjar, C. / Arnoux, P. | ||||||
Funding support | France, 1items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2019 Title: Control by Metals of Staphylopine Dehydrogenase Activity during Metallophore Biosynthesis. Authors: Hajjar, C. / Fanelli, R. / Laffont, C. / Brutesco, C. / Cullia, G. / Tribout, M. / Nurizzo, D. / Borezee-Durant, E. / Voulhoux, R. / Pignol, D. / Lavergne, J. / Cavelier, F. / Arnoux, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6h31.cif.gz | 195.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6h31.ent.gz | 154.5 KB | Display | PDB format |
PDBx/mmJSON format | 6h31.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6h31_validation.pdf.gz | 798.3 KB | Display | wwPDB validaton report |
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Full document | 6h31_full_validation.pdf.gz | 813.2 KB | Display | |
Data in XML | 6h31_validation.xml.gz | 37.3 KB | Display | |
Data in CIF | 6h31_validation.cif.gz | 53.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h3/6h31 ftp://data.pdbj.org/pub/pdb/validation_reports/h3/6h31 | HTTPS FTP |
-Related structure data
Related structure data | 6gmzSC 6h3dC 6h3fC 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
#1: Protein | Mass: 51198.660 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) Gene: RK60_12795, RK98_07680, RL06_05590, SAMEA3448991_00758 Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1K7Y513, UniProt: A0A0H3JT80*PLUS #2: Chemical | #3: Chemical | ChemComp-GOL / | #4: 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: 3.32 Å3/Da / Density % sol: 63 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.15 M Potassium bromide, 30% PEG MME 2000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 1, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97242 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→77 Å / Num. obs: 178459 / % possible obs: 98.3 % / Redundancy: 3 % / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 2.3→2.42 Å / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6GMZ Resolution: 2.3→19.98 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.906 / SU B: 6.623 / SU ML: 0.157 / Cross valid method: THROUGHOUT / ESU R: 0.236 / ESU R Free: 0.209 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.488 Å2
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Refinement step | Cycle: 1 / Resolution: 2.3→19.98 Å
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Refine LS restraints |
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