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- PDB-4iud: Crystal structure of an O2-tolerant [NiFe]-hydrogenase from Ralst... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4iud | ||||||
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Title | Crystal structure of an O2-tolerant [NiFe]-hydrogenase from Ralstonia eutropha in its as-isolated form with ascorbate - partly reduced state | ||||||
![]() | (Uptake hydrogenase ...) x 2 | ||||||
![]() | OXIDOREDUCTASE / [NiFe] hydrogenase / Knallgas bacteria / proteobacteria / aerobic hydrogen bacteria / hydrogen catalysis / metalloenzyme / metalloprotein catalytic center / nickel-iron cofactor / bimetallic / Ni-Fe active site / iron-sulfur cluster / [4Fe-3S] cluster / [3Fe-4S] cluster / [4Fe-4S] cluster / reduced state / oxidized state / oxygen-tolerant hydrogenase / membrane-bound | ||||||
Function / homology | ![]() hydrogenase (acceptor) / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase complex / hydrogenase (acceptor) activity / ferredoxin hydrogenase activity / anaerobic respiration / 3 iron, 4 sulfur cluster binding / nickel cation binding / 4 iron, 4 sulfur cluster binding / electron transfer activity ...hydrogenase (acceptor) / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase complex / hydrogenase (acceptor) activity / ferredoxin hydrogenase activity / anaerobic respiration / 3 iron, 4 sulfur cluster binding / nickel cation binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hammer, M. / Schmidt, A. / Frielingsdorf, S. / Fritsch, J. / Lenz, O. / Scheerer, P. | ||||||
![]() | ![]() Title: Reversible [4Fe-3S] cluster morphing in an O2-tolerant [NiFe] hydrogenase. Authors: Frielingsdorf, S. / Fritsch, J. / Schmidt, A. / Hammer, M. / Lowenstein, J. / Siebert, E. / Pelmenschikov, V. / Jaenicke, T. / Kalms, J. / Rippers, Y. / Lendzian, F. / Zebger, I. / Teutloff, ...Authors: Frielingsdorf, S. / Fritsch, J. / Schmidt, A. / Hammer, M. / Lowenstein, J. / Siebert, E. / Pelmenschikov, V. / Jaenicke, T. / Kalms, J. / Rippers, Y. / Lendzian, F. / Zebger, I. / Teutloff, C. / Kaupp, M. / Bittl, R. / Hildebrandt, P. / Friedrich, B. / Lenz, O. / Scheerer, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 399.9 KB | Display | ![]() |
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PDB format | ![]() | 322.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 489 KB | Display | ![]() |
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Full document | ![]() | 491.9 KB | Display | |
Data in XML | ![]() | 41.2 KB | Display | |
Data in CIF | ![]() | 64.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4iubC ![]() 4iucC ![]() 3rgwS 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
-Uptake hydrogenase ... , 2 types, 2 molecules LS
#1: Protein | Mass: 67263.195 Da / Num. of mol.: 1 / Fragment: UNP residues 1-603 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain (production host): ATCC 17699 / H16 / DSM 428 / Stanier 337 References: UniProt: P31891, EC: 1.12.5.1 |
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#2: Protein | Mass: 37384.520 Da / Num. of mol.: 1 / Fragment: UNP residues 44-360 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain (production host): ATCC 17699 / H16 / DSM 428 / Stanier 337 References: UniProt: P31892, EC: 1.12.5.1 |
-Non-polymers , 7 types, 988 molecules ![](data/chem/img/NFV.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/F3S.gif)
![](data/chem/img/S3F.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/F3S.gif)
![](data/chem/img/S3F.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-NFV / |
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#4: Chemical | ChemComp-MG / |
#5: Chemical | ChemComp-SF4 / |
#6: Chemical | ChemComp-F3S / |
#7: Chemical | ChemComp-S3F / |
#8: Chemical | ChemComp-CL / |
#9: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.64 % |
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Crystal grow | Temperature: 282 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 20-30% PEG3350, 100 mM Bis-Tris methane, pH 5.5, crystal soaked in ascorbate, VAPOR DIFFUSION, SITTING DROP, temperature 282K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Jun 17, 2011 / Details: mirrors |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→34.42 Å / Num. obs: 150757 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 14.92 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 1.45→1.53 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.699 / Mean I/σ(I) obs: 2.1 / Num. unique all: 21043 / Rsym value: 0.699 / % possible all: 96.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3RGW Resolution: 1.45→34.42 Å / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.887 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→34.42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.45→1.488 Å / Total num. of bins used: 20
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