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Yorodumi- PDB-6h3f: Staphylopine dehydrogenase in complex with staphylopine and NADP+ -
+Open data
-Basic information
Entry | Database: PDB / ID: 6h3f | ||||||
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Title | Staphylopine dehydrogenase in complex with staphylopine and NADP+ | ||||||
Components | Staphylopine dehydrogenase | ||||||
Keywords | BIOSYNTHETIC PROTEIN / staphylopine biosynthesis | ||||||
Function / homology | staphylopine dehydrogenase / Opine metallophore dehydrogenase / Staphylopine dehydrogenase / oxidoreductase activity / Chem-8UX / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Uncharacterized protein / Staphylopine synthase Function and homology information | ||||||
Biological species | Staphylococcus aureus subsp. aureus N315 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 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 | 6h3f.cif.gz | 109.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6h3f.ent.gz | 81.9 KB | Display | PDB format |
PDBx/mmJSON format | 6h3f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h3/6h3f ftp://data.pdbj.org/pub/pdb/validation_reports/h3/6h3f | HTTPS FTP |
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-Related structure data
Related structure data | 6gmzSC 6h31C 6h3dC 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 51198.660 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus subsp. aureus N315 (bacteria) Gene: SA2256 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H3JNH9, UniProt: A0A0H3JT80*PLUS |
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-Non-polymers , 5 types, 115 molecules
#2: Chemical | ChemComp-NAP / |
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#3: Chemical | ChemComp-8UX / ( |
#4: Chemical | ChemComp-GOL / |
#5: Chemical | ChemComp-PG4 / |
#6: 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: 2.64 Å3/Da / Density % sol: 53.35 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M ammonium acetate, 20-25% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Apr 24, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.966 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→93.59 Å / Num. obs: 118664 / % possible obs: 99.4 % / Redundancy: 4.2 % / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 2.2→2.25 Å / Mean I/σ(I) obs: 2.2 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6GMZ Resolution: 2.21→93.59 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.919 / SU B: 12.24 / SU ML: 0.271 / Cross valid method: THROUGHOUT / ESU R: 0.279 / ESU R Free: 0.244 / 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: 57.585 Å2
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Refinement step | Cycle: 1 / Resolution: 2.21→93.59 Å
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Refine LS restraints |
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