+Open data
-Basic information
Entry | Database: PDB / ID: 6c4r | ||||||||||||
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Title | Staphylopine dehydrogenase (SaODH) - Apo | ||||||||||||
Components | Staphylopine dehydrogenase | ||||||||||||
Keywords | OXIDOREDUCTASE / Opine Dehydrogenase Metallophore Siderophore / Yersinopine Pseudopaline Staphylopine | ||||||||||||
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: 2.288 Å | ||||||||||||
Authors | McFarlane, J.S. / Davis, C.L. / Lamb, A.L. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: J. Biol. Chem. / Year: 2018 Title: Staphylopine, pseudopaline, and yersinopine dehydrogenases: A structural and kinetic analysis of a new functional class of opine dehydrogenase. Authors: McFarlane, J.S. / Davis, C.L. / Lamb, A.L. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6c4r.cif.gz | 173.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6c4r.ent.gz | 139.5 KB | Display | PDB format |
PDBx/mmJSON format | 6c4r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c4/6c4r ftp://data.pdbj.org/pub/pdb/validation_reports/c4/6c4r | HTTPS FTP |
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-Related structure data
Related structure data | 6c4lC 6c4mC 6c4nC 6c4tSC 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: 52221.676 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: AB466_12420, AB526_12775, AFP37_00945, APW47_05390 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Q4GXD5, UniProt: A0A0H3JT80*PLUS | ||||
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#2: Chemical | #3: Chemical | ChemComp-SO4 / #4: 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: 2.71 Å3/Da / Density % sol: 54.55 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 100 mM sodium citrate HCl pH 5.6, 200 mM ammonium sulfate, 25% (w/v) PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 13, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.29→38.63 Å / Num. obs: 25087 / % possible obs: 99.1 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 2.29→2.37 Å / Rmerge(I) obs: 0.86 / Num. unique obs: 2343 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6C4T Resolution: 2.288→38.625 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.77 / 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: 2.288→38.625 Å
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Refine LS restraints |
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LS refinement shell |
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