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- PDB-5jsh: The 3D structure of recombinant [NiFeSe] hydrogenase from Desulfo... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5jsh | ||||||||||||
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Title | The 3D structure of recombinant [NiFeSe] hydrogenase from Desulfovibrio Vulgaris Hildenborough in the oxidized state at 1.30 Angstrom | ||||||||||||
![]() | (Periplasmic [NiFeSe] hydrogenase, ...) x 2 | ||||||||||||
![]() | OXIDOREDUCTASE / hydrogenase / biological hydrogen production | ||||||||||||
Function / homology | ![]() cytochrome-c3 hydrogenase / cytochrome-c3 hydrogenase activity / ferredoxin hydrogenase / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase complex / ferredoxin hydrogenase activity / anaerobic respiration / cell envelope / 3 iron, 4 sulfur cluster binding / nickel cation binding ...cytochrome-c3 hydrogenase / cytochrome-c3 hydrogenase activity / ferredoxin hydrogenase / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase complex / ferredoxin hydrogenase activity / anaerobic respiration / cell envelope / 3 iron, 4 sulfur cluster binding / nickel cation binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / periplasmic space / membrane / metal ion binding Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Marques, M.C. / Pereira, I.A.C. / Matias, P.M. | ||||||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 465.1 KB | Display | ![]() |
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PDB format | ![]() | 379.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 488.5 KB | Display | ![]() |
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Full document | ![]() | 489.2 KB | Display | |
Data in XML | ![]() | 36 KB | Display | |
Data in CIF | ![]() | 56.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5jskC ![]() 5jsuC ![]() 5jsyC ![]() 5jt1C ![]() 2wpnS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() Gene: hysB, DVU_1917 Production host: ![]() References: UniProt: Q72AS4, ferredoxin hydrogenase |
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#2: Protein | Mass: 55989.047 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Cysteine 75 is oxidized to sulfenate (CSD) in the crystal structure Source: (gene. exp.) ![]() Gene: hysA, DVU_1918 Production host: ![]() References: UniProt: Q72AS3, ferredoxin hydrogenase |
-Non-polymers , 8 types, 865 molecules 














#3: Chemical | #4: Chemical | ChemComp-6ML / | #5: Chemical | ChemComp-FCO / | #6: Chemical | ChemComp-NI / | #7: Chemical | ChemComp-FE2 / | #8: Chemical | ChemComp-H2S / | #9: Chemical | ChemComp-CL / | #10: Water | ChemComp-HOH / | |
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-Details
Has protein modification | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.59 % / 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: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 7, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9334 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→54 Å / Num. obs: 169426 / % possible obs: 96.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 8.6 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.061 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 1.3→1.32 Å / Redundancy: 2 % / Rmerge(I) obs: 0.315 / Mean I/σ(I) obs: 2.2 / % possible all: 70.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2WPN Resolution: 1.3→51.819 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 0.68 / Phase error: 13.22 / Stereochemistry target values: ML Details: THE ANOMALOUS DISPERSION PARAMETERS FOR THE SE ATOM WERE REFINED. HYDROGEN ATOMS WERE ADDED IN CALCULATED POSITIONS AND REFINED IN RIDING POSITIONS. INDIVIDUAL ANISOTROPIC ATOMIC ...Details: THE ANOMALOUS DISPERSION PARAMETERS FOR THE SE ATOM WERE REFINED. HYDROGEN ATOMS WERE ADDED IN CALCULATED POSITIONS 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 / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→51.819 Å
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Refine LS restraints |
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LS refinement shell |
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