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Yorodumi- PDB-5jsy: The 3D structure of the Ni-reconstituted U489C variant of [NiFeSe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jsy | ||||||||||||
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Title | The 3D structure of the Ni-reconstituted U489C variant of [NiFeSe] hydrogenase from Desulfovibrio vulgaris Hildenborough at 1.04 Angstrom resolution | ||||||||||||
Components | (Periplasmic [NiFeSe] hydrogenase, ...) x 2 | ||||||||||||
Keywords | OXIDOREDUCTASE / NIFESE-SITE H2 CLEAVAGE/PRODUCTION | ||||||||||||
Function / homology | Function and homology information cytochrome-c3 hydrogenase / ferredoxin 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 ...cytochrome-c3 hydrogenase / ferredoxin 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 vulgaris str. Hildenborough (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.04 Å | ||||||||||||
Authors | Marques, M.C. / Pereira, I.A.C. / Matias, P.M. | ||||||||||||
Funding support | Portugal, 3items
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Citation | Journal: Nat. Chem. Biol. / Year: 2017 Title: The direct role of selenocysteine in [NiFeSe] hydrogenase maturation and catalysis. Authors: Marques, M.C. / Tapia, C. / Gutierrez-Sanz, O. / Ramos, A.R. / Keller, K.L. / Wall, J.D. / De Lacey, A.L. / Matias, P.M. / Pereira, I.A.C. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jsy.cif.gz | 470.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jsy.ent.gz | 385.5 KB | Display | PDB format |
PDBx/mmJSON format | 5jsy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5jsy_validation.pdf.gz | 481.3 KB | Display | wwPDB validaton report |
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Full document | 5jsy_full_validation.pdf.gz | 482.8 KB | Display | |
Data in XML | 5jsy_validation.xml.gz | 38.1 KB | Display | |
Data in CIF | 5jsy_validation.cif.gz | 60.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/js/5jsy ftp://data.pdbj.org/pub/pdb/validation_reports/js/5jsy | HTTPS FTP |
-Related structure data
Related structure data | 5jshC 5jskC 5jsuC 5jt1C 2wpnS 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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Unit cell |
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-Components
-Periplasmic [NiFeSe] hydrogenase, ... , 2 types, 2 molecules AB
#1: Protein | Mass: 33940.879 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desulfovibrio vulgaris str. Hildenborough (bacteria) Gene: hysB, DVU_1917 Production host: Desulfovibrio vulgaris str. Hildenborough (bacteria) References: UniProt: Q72AS4, ferredoxin hydrogenase |
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#2: Protein | Mass: 55958.148 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desulfovibrio vulgaris str. Hildenborough (bacteria) Gene: hysA, DVU_1918 Production host: Desulfovibrio vulgaris str. Hildenborough (bacteria) References: UniProt: Q72AS3, ferredoxin hydrogenase |
-Non-polymers , 7 types, 996 molecules
#3: Chemical | #4: Chemical | ChemComp-FCO / | #5: Chemical | ChemComp-NI / | #6: Chemical | ChemComp-FE2 / | #7: Chemical | ChemComp-H2S / | #8: Chemical | ChemComp-CL / | #9: 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: 1.99 Å3/Da / Density % sol: 38.14 % / Description: irregular hexagonal plate |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 1500 (w/v) and 0.1 mM Tris-HCl pH 7.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 17, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.04→29.2 Å / Num. obs: 326274 / % possible obs: 96.9 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 1.04→1.06 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.879 / Mean I/σ(I) obs: 1.6 / % possible all: 87.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2WPN Resolution: 1.04→29.2 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.07 / Phase error: 11.76 Details: Hydrogen atoms in calculated positions were included and refined in riding positions. Individual anisotropic atomic displacement parameters for all protein non-hydrogen atoms were refined.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.04→29.2 Å
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Refine LS restraints |
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LS refinement shell |
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