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- PDB-4kl8: High-resolution structure of anaerobically purified Dm. baculatum... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4kl8 | ||||||||||||
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Title | High-resolution structure of anaerobically purified Dm. baculatum [NiFeSe]-hydrogenase after crystallization under air | ||||||||||||
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![]() | OXIDOREDUCTASE / O2-resistance / H2-cleavage and production / SELENINATE | ||||||||||||
Function / homology | ![]() hydrogenase (acceptor) / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase complex / hydrogenase (acceptor) activity / ferredoxin hydrogenase activity / anaerobic respiration / nickel cation binding / 4 iron, 4 sulfur cluster binding / periplasmic space / electron transfer activity ...hydrogenase (acceptor) / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase complex / hydrogenase (acceptor) activity / ferredoxin hydrogenase activity / anaerobic respiration / nickel cation binding / 4 iron, 4 sulfur cluster binding / periplasmic space / electron transfer activity / membrane / metal ion binding Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Volbeda, A. / Cavazza, C. / Fontecilla-Camps, J.C. | ||||||||||||
![]() | ![]() Title: Structural foundations for the O2 resistance of Desulfomicrobium baculatum [NiFeSe]-hydrogenase. Authors: Volbeda, A. / Amara, P. / Iannello, M. / De Lacey, A.L. / Cavazza, C. / Fontecilla-Camps, J.C. #1: ![]() Title: The crystal structure of a reduced [NiFeSe] hydrogenase provides an image of the activated catalytic center. Authors: Garcin, E. / Vernede, X. / Hatchikian, E.C. / Volbeda, A. / Frey, M. / Fontecilla-Camps, J.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 | ![]() | 700.3 KB | Display | ![]() |
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PDB format | ![]() | 567.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4kn9C ![]() 4ko1C ![]() 4ko2C ![]() 4ko3C ![]() 4ko4C ![]() 1cc1S 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 2 types, 4 molecules STLM
#1: Protein | Mass: 30874.131 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Protein | Mass: 55323.840 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Non-polymers , 8 types, 1869 molecules ![](data/chem/img/SF4.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/FCO.gif)
![](data/chem/img/NI.gif)
![](data/chem/img/H2S.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/FCO.gif)
![](data/chem/img/NI.gif)
![](data/chem/img/H2S.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-SF4 / #4: Chemical | ChemComp-CA / #5: Chemical | ChemComp-CL / | #6: Chemical | ChemComp-GOL / #7: Chemical | #8: Chemical | #9: Chemical | #10: Water | ChemComp-HOH / | |
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-Details
Sequence details | RESIDUES L 492 AND M 492 HAVE THREE STATES: SE7 = OXIDIZED TO SELENINATE (O=SE-O, CONFORMATION ...RESIDUES L 492 AND M 492 HAVE THREE STATES: SE7 = OXIDIZED TO SELENINATE |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.23 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 22-27% PEG 4000, 0.2M CaCl2, 0.1M Tris/HCl, under air, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 18, 2010 |
Radiation | Monochromator: two crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.52→30 Å / Num. all: 242003 / Num. obs: 226689 / % possible obs: 91.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 17.3 Å2 / Rsym value: 0.057 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 1.52→1.6 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 22885 / Rsym value: 0.375 / % possible all: 66.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1CC1 Resolution: 1.52→25 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.629 / SU ML: 0.043 / Isotropic thermal model: anisotropic temperature factors / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.077 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.769 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.52→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.52→1.559 Å / Total num. of bins used: 20
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