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- PDB-3ze6: 3D structure of the Ni-Fe-Se hydrogenase from D. vulgaris Hildenb... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3ze6 | |||||||||||||||
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Title | 3D structure of the Ni-Fe-Se hydrogenase from D. vulgaris Hildenborough in the as-isolated oxidized state at 1.50 Angstroms | |||||||||||||||
![]() | (PERIPLASMIC [NIFESE] HYDROGENASE, ...) x 2 | |||||||||||||||
![]() | OXIDOREDUCTASE / HYDROGENASE BIOHYDROGEN OXYGEN TOLERANCE | |||||||||||||||
Function / homology | ![]() 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 | ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Marques, M.C. / Coelho, R. / Pereira, I.A.C. / Matias, P.M. | |||||||||||||||
![]() | ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 318 KB | Display | ![]() |
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PDB format | ![]() | 257.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 979.8 KB | Display | ![]() |
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Full document | ![]() | 994.3 KB | Display | |
Data in XML | ![]() | 35.7 KB | Display | |
Data in CIF | ![]() | 54.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3ze7C ![]() 3ze8C ![]() 3ze9C ![]() 3zeaC ![]() 2wpnS C: citing same article ( S: Starting model for refinement |
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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: 30293.635 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: Protein | Mass: 53431.121 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: CYSTEINE B 75 IS OXIDIZED TO CYSTEINE SULFINIC ACID Source: (natural) ![]() |
-Non-polymers , 9 types, 714 molecules ![](data/chem/img/SF4.gif)
![](data/chem/img/FSX.gif)
![](data/chem/img/SBY.gif)
![](data/chem/img/FCO.gif)
![](data/chem/img/NI.gif)
![](data/chem/img/FE2.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FSX.gif)
![](data/chem/img/SBY.gif)
![](data/chem/img/FCO.gif)
![](data/chem/img/NI.gif)
![](data/chem/img/FE2.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-FSX / | #5: Chemical | ChemComp-SBY / #6: Chemical | ChemComp-FCO / | #7: Chemical | ChemComp-NI / | #8: Chemical | ChemComp-FE2 / | #9: Chemical | ChemComp-CL / | #10: Chemical | ChemComp-GOL / | #11: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | FSX RESIDUE REPRESENTS THE PARTIAL OXIDATION OF THE CANONICAL FE4S4 CUBANE CLUSTER TO FE4S3O3. THE ...FSX RESIDUE REPRESENTS |
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Sequence details | SIGNAL PEPTIDE CLEAVED OFF MATURE PROTEIN |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.6 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 7.5 Details: CRYSTALS WERE GROWN BY THE SITTING DROP VAPOR DIFFUSION METHOD, BY MIXING 1.5 UL OF RESERVOIR SOLUTION CONTAINING 20% POLYETHYLENE GLYCOL (PEG) 1500, 0.1 M TRIS-HCL, PH 8.5 AND AN EQUAL ...Details: CRYSTALS WERE GROWN BY THE SITTING DROP VAPOR DIFFUSION METHOD, BY MIXING 1.5 UL OF RESERVOIR SOLUTION CONTAINING 20% POLYETHYLENE GLYCOL (PEG) 1500, 0.1 M TRIS-HCL, PH 8.5 AND AN EQUAL VOLUME OF A SOLUTION COMPOSED OF 10 MG/ML OF PROTEIN IN 10 MM TRIS-HCL BUFFER AT PH 7.6. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 18, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→45.5 Å / Num. obs: 114933 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 10.02 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 1.5→1.54 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 3 / % possible all: 88.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2WPN Resolution: 1.5→45.512 Å / SU ML: 0.13 / σ(F): 0.83 / Phase error: 13.55 / Stereochemistry target values: ML / Details: REFINEMENT PROTOCOL USED ANOMALOUS DIFFERENCES
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Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.418 Å2 / ksol: 0.352 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.5→45.512 Å
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Refine LS restraints |
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LS refinement shell |
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