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Yorodumi- PDB-3ze9: 3D structure of the NiFeSe hydrogenase from D. vulgaris Hildenbor... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ze9 | |||||||||
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Title | 3D structure of the NiFeSe hydrogenase from D. vulgaris Hildenborough in the oxidized as-isolated state at 1.33 Angstroms | |||||||||
Components | (PERIPLASMIC [NIFESE] HYDROGENASE, ...) x 2 | |||||||||
Keywords | OXIDOREDUCTASE / HYDROGENASE BIOHYDROGEN OXYGEN TOLERANCE | |||||||||
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: 1.33 Å | |||||||||
Authors | Marques, M.C. / Coelho, R. / Pereira, I.A.C. / Matias, P.M. | |||||||||
Citation | Journal: Int.J.Hydrogen Energy / Year: 2013 Title: Redox State-Dependent Changes in the Crystal Structure of [Nifese] Hydrogenase from Desulfovibrio Vulgaris Hildenborough Authors: Marques, M.C. / Coelho, R. / Pereira, I.A.C. / Matias, P.M. #1: Journal: J.Mol.Biol. / Year: 2010 Title: The Three-Dimensional Structure of [Nifese] Hydrogenase from Desulfovibrio Vulgaris Hildenborough: A Hydrogenase without a Bridging Ligand in the Active Site in its Oxidised, "as-Isolated" State. Authors: Marques, M.C. / Coelho, R. / De Lacey, A.L. / 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 | 3ze9.cif.gz | 458.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ze9.ent.gz | 381.8 KB | Display | PDB format |
PDBx/mmJSON format | 3ze9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ze/3ze9 ftp://data.pdbj.org/pub/pdb/validation_reports/ze/3ze9 | HTTPS FTP |
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-Related structure data
Related structure data | 3ze6C 3ze7C 3ze8C 3zeaC 2wpnS 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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Unit cell |
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Components on special symmetry positions |
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-Components
-PERIPLASMIC [NIFESE] HYDROGENASE, ... , 2 types, 2 molecules AB
#1: Protein | Mass: 30293.635 Da / Num. of mol.: 1 / Fragment: RESIDUES 35-317 / Source method: isolated from a natural source / Source: (natural) DESULFOVIBRIO VULGARIS (bacteria) / Strain: HILDENBOROUGH / References: UniProt: Q72AS4, ferredoxin hydrogenase |
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#2: Protein | Mass: 53431.121 Da / Num. of mol.: 1 / Fragment: RESIDUES 12-495 / Source method: isolated from a natural source / Source: (natural) DESULFOVIBRIO VULGARIS (bacteria) / Strain: HILDENBOROUGH / References: UniProt: Q72AS3, ferredoxin hydrogenase |
-Non-polymers , 7 types, 748 molecules
#3: Chemical | #4: Chemical | ChemComp-FSX / | #5: Chemical | ChemComp-FCO / | #6: Chemical | ChemComp-NI / | #7: Chemical | ChemComp-FE2 / | #8: Chemical | ChemComp-CL / | #9: Water | ChemComp-HOH / | |
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-Details
Sequence details | SIGNAL PEPTIDE CLEAVED OFF MATURE PROTEIN |
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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: 2.12 Å3/Da / Density % sol: 42 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 4.1 Details: CRYSTALS WERE OBTAINED USING THE SITTING-DROP VAPOR DIFFUSION METHOD. 1 UL OF A RESERVOIR SOLUTION CONTAINING 16% PEG 8000 (W/V) AND 0.05 M KH2PO4 PH 4.1 WAS MIXED WITH AN EQUAL VOLUME OF A ...Details: CRYSTALS WERE OBTAINED USING THE SITTING-DROP VAPOR DIFFUSION METHOD. 1 UL OF A RESERVOIR SOLUTION CONTAINING 16% PEG 8000 (W/V) AND 0.05 M KH2PO4 PH 4.1 WAS MIXED WITH AN EQUAL VOLUME OF A SOLUTION COMPOSED OF 11 MG/ML PROTEIN IN 20 MM TRIS-HCL BUFFER PH 7.6, AND EQUILIBRATED AGAINST A 500 UL RESERVOIR. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 21, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 1.33→53.9 Å / Num. obs: 159127 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 1.33→1.41 Å / Redundancy: 3 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 1.7 / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WPN Resolution: 1.33→52.895 Å / SU ML: 0.11 / σ(F): 1.25 / Phase error: 15.07 / Stereochemistry target values: ML Details: REFINEMENT PROTOCOL USED SEPARATE FRIEDEL PAIRS. TOTAL NUMBER OF REFLECTIONS 301432.
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Solvent computation | Shrinkage radii: 1.1 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.33→52.895 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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