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Yorodumi- PDB-4uqp: High-resolution structure of the D. fructosovorans NiFe-hydrogena... -
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-Basic information
Entry | Database: PDB / ID: 4uqp | ||||||
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Title | High-resolution structure of the D. fructosovorans NiFe-hydrogenase L122A mutant after exposure to air | ||||||
Components | (PERIPLASMIC [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 / ferredoxin hydrogenase complex / ferredoxin hydrogenase activity / 3 iron, 4 sulfur cluster binding / nickel cation binding / 4 iron, 4 sulfur cluster binding / periplasmic space / metal ion binding Similarity search - Function | ||||||
Biological species | DESULFOVIBRIO FRUCTOSOVORANS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 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. / 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 | 4uqp.cif.gz | 697.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uqp.ent.gz | 574.9 KB | Display | PDB format |
PDBx/mmJSON format | 4uqp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uq/4uqp ftp://data.pdbj.org/pub/pdb/validation_reports/uq/4uqp | HTTPS FTP |
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-Related 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
-PERIPLASMIC [NIFE] HYDROGENASE ... , 2 types, 4 molecules ABQR
#1: Protein | Mass: 28418.389 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 50-314 Source method: isolated from a genetically manipulated source Source: (gene. exp.) DESULFOVIBRIO FRUCTOSOVORANS (bacteria) Production host: DESULFOVIBRIO FRUCTOSOVORANS (bacteria) / References: UniProt: P18187, cytochrome-c3 hydrogenase #2: Protein | Mass: 61190.777 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) DESULFOVIBRIO FRUCTOSOVORANS (bacteria) Production host: DESULFOVIBRIO FRUCTOSOVORANS (bacteria) / References: UniProt: P18188, cytochrome-c3 hydrogenase |
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-Non-polymers , 10 types, 1712 molecules
#3: Chemical | ChemComp-SF4 / #4: Chemical | #5: Chemical | ChemComp-GOL / #6: Chemical | ChemComp-SOT / | #7: Chemical | ChemComp-H2S / | #8: Chemical | #9: Chemical | #10: Chemical | #11: Chemical | #12: Water | ChemComp-HOH / | |
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-Details
Sequence details | L122A MUTATION AND N-TERMINAL STREP-TAG IN LARGE SUBUNIT |
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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: 2.03 Å3/Da / Density % sol: 39.6 % / Description: NONE |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 6.1 Details: VAPOR DIFFUSION, ANAEROBIC GROWTH, 298 K, PEG 6000, MES, HEPES, CRYSTAL EXPOSED 3 DAYS TO AIR, PH 6.1 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97618 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 12, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97618 Å / Relative weight: 1 |
Reflection | Resolution: 1.42→44.1 Å / Num. obs: 264128 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Redundancy: 3.59 % / Biso Wilson estimate: 16.7 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 11.48 |
Reflection shell | Resolution: 1.42→1.5 Å / Redundancy: 2.83 % / Rmerge(I) obs: 0.337 / Mean I/σ(I) obs: 2.4 / % possible all: 86.4 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.42→30 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.962 / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.055 / 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: 13.199 Å2
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Refinement step | Cycle: LAST / Resolution: 1.42→30 Å
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Refine LS restraints |
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