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Yorodumi- PDB-6z8j: Structure of [NiFeSe] hydrogenase from Desulfovibrio vulgaris hil... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6z8j | |||||||||
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Title | Structure of [NiFeSe] hydrogenase from Desulfovibrio vulgaris hildenborough pressurized with Oxygen gas - structure wtO2 | |||||||||
Components | (Periplasmic [NiFeSe] hydrogenase, ...) x 2 | |||||||||
Keywords | OXIDOREDUCTASE / Hydrogenase / Selenium / gas channels / high-pressure derivatization | |||||||||
Function / homology | Function and homology information cytochrome-c3 hydrogenase / ferredoxin 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 vulgaris (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.09 Å | |||||||||
Authors | Zacarias, S. / Temporao, A. / Carpentier, P. / van der Linden, P. / Pereira, I.A.C. / Matias, P.M. | |||||||||
Funding support | Portugal, 2items
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Citation | Journal: J.Biol.Inorg.Chem. / Year: 2020 Title: Exploring the gas access routes in a [NiFeSe] hydrogenase using crystals pressurized with krypton and oxygen. Authors: Zacarias, S. / Temporao, A. / Carpentier, P. / van der Linden, P. / Pereira, I.A.C. / Matias, P.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6z8j.cif.gz | 1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6z8j.ent.gz | 722.5 KB | Display | PDB format |
PDBx/mmJSON format | 6z8j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z8/6z8j ftp://data.pdbj.org/pub/pdb/validation_reports/z8/6z8j | HTTPS FTP |
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-Related structure data
Related structure data | 6z7rC 6z8mC 6z8oC 6z9gC 6z9oC 6za1C 5jskS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.5281/zenodo.3872130 / Data set type: diffraction image 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 [NiFeSe] hydrogenase, ... , 2 types, 4 molecules ACBD
#1: Protein | Mass: 30261.568 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303) (bacteria) Strain: Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303 / Gene: hysB, DVU_1917 Production host: Desulfovibrio vulgaris str. Hildenborough (bacteria) References: UniProt: Q72AS4, ferredoxin hydrogenase #2: Protein | Mass: 53383.059 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303) (bacteria) Strain: Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303 / Gene: hysA, DVU_1918 Production host: Desulfovibrio vulgaris str. Hildenborough (bacteria) References: UniProt: Q72AS3, ferredoxin hydrogenase |
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-Non-polymers , 10 types, 1037 molecules
#3: Chemical | ChemComp-SF4 / #4: Chemical | #5: Chemical | ChemComp-GOL / #6: Chemical | #7: Chemical | #8: Chemical | #9: Chemical | #10: Chemical | #11: Chemical | #12: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 1.75 Å3/Da / Density % sol: 29.7 % / Description: thin plate |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.6 / Details: 20% PEG 1500 (w/v) and 0.1 mM Tris-HCl pH 7.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 2, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.09→98.5 Å / Num. obs: 354735 / % possible obs: 62.9 % / Redundancy: 2.2 % / Biso Wilson estimate: 9.7 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.047 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 1.09→1.11 Å / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 17734 / CC1/2: 0.658 / Rpim(I) all: 0.423 / % possible all: 15.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5JSK Resolution: 1.09→42.41 Å / SU ML: 0.093 / Cross valid method: FREE R-VALUE / σ(F): 0.86 / Phase error: 19.6961 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 Details: Hydrogen atoms were included in calculated positions, solvent molecules were added manually in COOT using 2|Fo|-|Fc| and |Fo|-|Fc| maps; occupancy factors were refined for disordered ...Details: Hydrogen atoms were included in calculated positions, solvent molecules were added manually in COOT using 2|Fo|-|Fc| and |Fo|-|Fc| maps; occupancy factors were refined for disordered residues and the O2 molecules; anomalous dispersion parameters were refined for the selenium atom in Sec 489; anisotropic atomic displacement parameters were refined for all non-hydrogen and non-solvent atoms.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.98 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.09→42.41 Å
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Refine LS restraints |
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LS refinement shell |
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