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Yorodumi- PDB-4upv: Low X-ray dose structure of a Ni-A Ni-Sox mixture of the D. fruct... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4upv | ||||||
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Title | Low X-ray dose structure of a Ni-A Ni-Sox mixture of the D. fructosovorans NiFe-hydrogenase L122A mutant | ||||||
Components | (NIFE-HYDROGENASE ...) x 2 | ||||||
Keywords | OXIDOREDUCTASE / NIFE-SITE / NI-A STATE / SULFENATE / NI-SOX STATE / PERSULFIDE | ||||||
Function / homology | Function and homology information cytochrome-c3 hydrogenase / cytochrome-c3 hydrogenase activity / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase complex / ferredoxin hydrogenase activity / anaerobic respiration / 3 iron, 4 sulfur cluster binding / nickel cation binding / 4 iron, 4 sulfur cluster binding / periplasmic space ...cytochrome-c3 hydrogenase / cytochrome-c3 hydrogenase activity / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase complex / ferredoxin hydrogenase activity / anaerobic respiration / 3 iron, 4 sulfur cluster binding / nickel cation binding / 4 iron, 4 sulfur cluster binding / periplasmic space / electron transfer activity / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | DESULFOVIBRIO FRUCTOSOVORANS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å | ||||||
Authors | Volbeda, A. / Martin, L. / Barbier, E. / Gutierrez-Sanz, O. / DeLacey, A.L. / Liebgott, P.P. / Dementin, S. / Rousset, M. / Fontecilla-Camps, J.C. | ||||||
Citation | Journal: J. Biol. Inorg. Chem. / Year: 2015 Title: Crystallographic studies of [NiFe]-hydrogenase mutants: towards consensus structures for the elusive unready oxidized states. Authors: Volbeda, A. / Martin, L. / Barbier, E. / Gutierrez-Sanz, O. / De Lacey, A.L. / Liebgott, P.P. / Dementin, S. / Rousset, M. / Fontecilla-Camps, J.C. #1: Journal: J.Biol.Inorg.Chem. / Year: 2005 Title: Structural Differences between the Ready and Unready Oxidized States of [Nife] Hydrogenases. Authors: Volbeda, A. / Martin, L. / Cavazza, C. / Matho, M. / Faber, B.W. / Roseboom, W. / Albracht, S.P.J. / Garcin, E. / Rousset, M. / Fontecilla-Camps, J.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4upv.cif.gz | 709 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4upv.ent.gz | 580.3 KB | Display | PDB format |
PDBx/mmJSON format | 4upv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4upv_validation.pdf.gz | 552.8 KB | Display | wwPDB validaton report |
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Full document | 4upv_full_validation.pdf.gz | 562.3 KB | Display | |
Data in XML | 4upv_validation.xml.gz | 75.1 KB | Display | |
Data in CIF | 4upv_validation.cif.gz | 116.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/up/4upv ftp://data.pdbj.org/pub/pdb/validation_reports/up/4upv | HTTPS FTP |
-Related structure data
Related structure data | 4upeC 4uqlC 4uqpC 4urhC 1yqwS C: citing same article (ref.) S: Starting model for refinement |
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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
-NIFE-HYDROGENASE ... , 2 types, 4 molecules ABQR
#1: Protein | Mass: 28418.389 Da / Num. of mol.: 2 / Fragment: RESIDUES 50-314 Source method: isolated from a genetically manipulated source Source: (gene. exp.) DESULFOVIBRIO FRUCTOSOVORANS (bacteria) Production host: DESULFOVIBRIO FRUCTOSOVORANS (bacteria) References: UniProt: E1K248, UniProt: P18187*PLUS, cytochrome-c3 hydrogenase #2: Protein | Mass: 61190.777 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-549 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) DESULFOVIBRIO FRUCTOSOVORANS (bacteria) Production host: DESULFOVIBRIO FRUCTOSOVORANS (bacteria) References: UniProt: E1K247, UniProt: P18188*PLUS, cytochrome-c3 hydrogenase |
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-Non-polymers , 11 types, 1763 molecules
#3: Chemical | ChemComp-SF4 / #4: Chemical | #5: Chemical | ChemComp-GOL / #6: Chemical | #7: Chemical | ChemComp-SOT / | #8: Chemical | ChemComp-H2S / | #9: Chemical | #10: Chemical | #11: Chemical | #12: Chemical | ChemComp-CL / | #13: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | IN THE UNREADY NI-A STATE NI(III) IS BOUND TO CYS72-SG, CSX75-OD (SULFENATE), CYS543-SG, O2001 AND ...IN THE UNREADY NI-A STATE NI(III) IS BOUND TO CYS72-SG, CSX75-OD (SULFENATE), CYS543-SG, O2001 AND CYS546-SG IN A DISTORTED SQUARE PYRAMIDAL COORDINATI |
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Sequence details | L122A MUTATION AND N-TERMINAL STREP-TAG |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.6 % / Description: NONE |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.1 Details: VAPOR DIFFUSION, ANAEROBIC, 298 K, PEG 6000, MES, HEPES, PH 6.1 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97974 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 26, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97974 Å / Relative weight: 1 |
Reflection | Resolution: 1.52→49.03 Å / Num. obs: 220781 / % possible obs: 90.6 % / Observed criterion σ(I): -3 / Redundancy: 3.55 % / Biso Wilson estimate: 16.6 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 12.83 |
Reflection shell | Resolution: 1.52→1.61 Å / Redundancy: 2.67 % / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 1.97 / % possible all: 59.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1YQW Resolution: 1.52→30 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.77 / SU ML: 0.044 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.546 Å2
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Refinement step | Cycle: LAST / Resolution: 1.52→30 Å
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Refine LS restraints |
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