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- PDB-7odg: Crystal structure of the O2-tolerant MBH-P242C from Ralstonia eut... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7odg | |||||||||
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Title | Crystal structure of the O2-tolerant MBH-P242C from Ralstonia eutropha in its reduced state | |||||||||
![]() | (Uptake hydrogenase ...) x 2 | |||||||||
![]() | ELECTRON TRANSPORT / NIFE / HYDROGENASE / KNALLGASBACTERIA / PROTEOBACTERIA / AEROBIC HYDROGEN BACTERIA / DEHYDROGENASE / OXIDOREDUCTASE / HYDROGEN CATALYSIS / METALLOENZYME / METALLOPROTEIN CATALYTIC CENTER / BIMETALLIC / NI-FE ACTIVE SITE / T-CLUSTER / REDUCED STATE / OXYGEN-TOLERANT HYDROGENASE / MEMBRANE / MEMBRANE-BOUND / OXIDOREDUCTASE-OXIDOREDUCTASE COMPLEX P242C / MEDIAL CLUSTER / ELECTRON RELAY / CUBANE CLUSTER / LOW POTENTIAL / CLUSTER TUNING | |||||||||
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 | ![]() ![]() ![]() | |||||||||
![]() | Schmidt, A. / Kalms, J. / Scheerer, P. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Resonance Raman spectroscopic analysis of the iron-sulfur cluster redox chain of the Ralstonia eutropha membrane-bound [NiFe]-hydrogenase Authors: Siebert, E. / Schmidt, A. / Frielingsdorf, S. / Kalms, J. / Kuhlmann, U. / Lenz, O. / Scheerer, P. / Zebger, I. / Hildebrandt, 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 | ![]() | 372.4 KB | Display | ![]() |
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PDB format | ![]() | 298.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438.2 KB | Display | ![]() |
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Full document | ![]() | 439.9 KB | Display | |
Data in XML | ![]() | 35 KB | Display | |
Data in CIF | ![]() | 51.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7odhC ![]() 3rgwS 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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Unit cell |
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Components
-Uptake hydrogenase ... , 2 types, 2 molecules LS
#1: Protein | Mass: 67247.195 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 17699 / H16 / DSM 428 / Stanier 337 / Gene: hoxG, PHG002 / Production host: ![]() |
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#2: Protein | Mass: 36049.051 Da / Num. of mol.: 1 / Mutation: P242C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 17699 / DSM 428 / KCTC 22496 / NCIMB 10442 / H16 / Stanier 337 Gene: hoxK, PHG001 / Production host: ![]() |
-Non-polymers , 6 types, 473 molecules ![](data/chem/img/NFU.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/F4S.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/F4S.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-NFU / | ||||||
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#4: Chemical | ChemComp-MG / | ||||||
#5: Chemical | #6: Chemical | ChemComp-F4S / | #7: Chemical | ChemComp-CL / | #8: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 40.13 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 25% PEG 3350 5.5-6.5 pH Bis-Tris |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC HF-4M / Detector: PIXEL / Date: Jun 24, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 1.62→75 Å / Num. obs: 110082 / % possible obs: 99.4 % / Redundancy: 5.1 % / CC1/2: 1 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 1.62→1.68 Å / Num. unique obs: 17545 / CC1/2: 0.91 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3RGW Resolution: 1.62→75 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.96 / SU B: 4.476 / SU ML: 0.067 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 60.88 Å2 / Biso mean: 22.445 Å2 / Biso min: 9.97 Å2
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Refinement step | Cycle: final / Resolution: 1.62→75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.62→1.662 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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