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Yorodumi- PDB-6nw0: Crystal Structure Desulfovibrio desulfuricans Nickel-Substituted ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6nw0 | ||||||
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Title | Crystal Structure Desulfovibrio desulfuricans Nickel-Substituted Rubredoxin | ||||||
Components | Rubredoxin | ||||||
Keywords | METAL BINDING PROTEIN / hydrogen evolution / hydrogenase / nickel / energy conversion | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Desulfovibrio desulfuricans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Slater, J.W. / Marguet, S.C. / Gray, M.E. / Sotomayor, M. / Shafaat, H.S. | ||||||
Funding support | United States, 1items
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Citation | Journal: Acs Catalysis / Year: 2019 Title: The Power of the Secondary Sphere: Modulating Hydrogenase Activity in Nickel-Substituted Rubredoxin Authors: Slater, J.W. / Marguet, S.C. / Gray, M.E. / Monaco, H.A. / Sotomayor, M. / Shafaat, H.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6nw0.cif.gz | 33 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6nw0.ent.gz | 20.9 KB | Display | PDB format |
PDBx/mmJSON format | 6nw0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nw/6nw0 ftp://data.pdbj.org/pub/pdb/validation_reports/nw/6nw0 | HTTPS FTP |
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-Related structure data
Related structure data | 6nw1C 6rxnS 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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2 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 5117.656 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desulfovibrio desulfuricans (bacteria) / Gene: SAMN02910291_00071, rd1 / Plasmid: pET21a / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A1K1LMQ8, UniProt: P04170*PLUS #2: Chemical | #3: 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: 2.11 Å3/Da / Density % sol: 41.59 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.3 / Details: 3.5 M ammonium sulfate, 0.1 M MES, 1.1% v/v MPD |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 17, 2018 |
Radiation | Monochromator: Cryogenically-cooled single crystal Si(220) side bounce Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→50 Å / Num. obs: 7302 / % possible obs: 91.9 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.082 / Rrim(I) all: 0.102 / Net I/σ(I): 12.61 |
Reflection shell | Resolution: 1.85→1.88 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.133 / Mean I/σ(I) obs: 8.38 / Num. unique obs: 311 / Rrim(I) all: 0.163 / % possible all: 94 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 6RXN Resolution: 1.85→32.53 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.934 / SU B: 2.968 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.151 / 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: 17.535 Å2
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Refinement step | Cycle: 1 / Resolution: 1.85→32.53 Å
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Refine LS restraints |
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