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Yorodumi- PDB-5mdk: Crystal structure of an O2-tolerant [NiFe]-hydrogenase from Ralst... -
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-Basic information
Entry | Database: PDB / ID: 5mdk | ||||||||||||
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Title | Crystal structure of an O2-tolerant [NiFe]-hydrogenase from Ralstonia eutropha in its as-isolated form (oxidized state - state 3) | ||||||||||||
Components | (Uptake hydrogenase ...) x 2 | ||||||||||||
Keywords | OXIDOREDUCTASE / [NIFE] HYDROGENASE / KNALLGASBACTERIA / PROTEOBACTERIA / AEROBIC HYDROGEN BACTERIA / DEHYDROGENASE / HYDROGEN CATALYSIS / METALLOENZYME / DIHYDROGEN / BIMETALLIC / METALLOPROTEIN CATALYTIC CENTER / NI-FE ACTIVE SITE / T-CLUSTER / FE-S CLUSTER / [4Fe-3S] CLUSTER / [3Fe-4S] CLUSTER / [4Fe-4S] CLUSTER / AS-ISOLATED STATE / OXIDIZED STATE / NATIVE / OXYGEN TOLERANT HYDROGENASE / MEMBRANE BOUND / MEMBRANE / HYDROPHOBIC TUNNEL / GAS TRANSPORT | ||||||||||||
Function / homology | Function and homology information 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 | Ralstonia eutropha H16 (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||||||||
Authors | Schmidt, A. / Kalms, J. / Scheerer, P. | ||||||||||||
Funding support | Germany, 2items
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Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018 Title: Tracking the route of molecular oxygen in O2-tolerant membrane-bound [NiFe] hydrogenase. Authors: Kalms, J. / Schmidt, A. / Frielingsdorf, S. / Utesch, T. / Gotthard, G. / von Stetten, D. / van der Linden, P. / Royant, A. / Mroginski, M.A. / Carpentier, P. / Lenz, O. / Scheerer, P. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mdk.cif.gz | 387 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mdk.ent.gz | 309.3 KB | Display | PDB format |
PDBx/mmJSON format | 5mdk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5mdk_validation.pdf.gz | 485.6 KB | Display | wwPDB validaton report |
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Full document | 5mdk_full_validation.pdf.gz | 488.5 KB | Display | |
Data in XML | 5mdk_validation.xml.gz | 37.3 KB | Display | |
Data in CIF | 5mdk_validation.cif.gz | 56.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/md/5mdk ftp://data.pdbj.org/pub/pdb/validation_reports/md/5mdk | HTTPS FTP |
-Related structure data
Related structure data | 5mdjC 5mdlC 3rgwS 4iubS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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.) Ralstonia eutropha H16 (bacteria) / Gene: HOXG / Production host: Ralstonia eutropha H16 (bacteria) / Strain (production host): H16 DSM 428 STANIER 337 / References: UniProt: P31891, hydrogenase (acceptor) |
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#2: Protein | Mass: 36027.023 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ralstonia eutropha H16 (bacteria) / Gene: HOXK / Production host: Ralstonia eutropha H16 (bacteria) / Strain (production host): H16 DSM 428 STANIER 337 / References: UniProt: P31892, hydrogenase (acceptor) |
-Non-polymers , 7 types, 660 molecules
#3: Chemical | ChemComp-MG / | ||||||||||
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#4: Chemical | #5: Chemical | ChemComp-NFV / | #6: Chemical | ChemComp-SF4 / | #7: Chemical | ChemComp-F3S / | #8: Chemical | ChemComp-F4S / | #9: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.31 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / Details: 20-30% PEG3350, 0.1M BIS-TRIS pH 5.5-6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97625 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 28, 2016 / Details: Mirrors |
Radiation | Monochromator: SI-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→47.78 Å / Num. obs: 134109 / % possible obs: 99.8 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.891 / Mean I/σ(I) obs: 1.9 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3RGW/4IUB Resolution: 1.5→47.78 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.978 / SU B: 2.833 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.057 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.66 Å2
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Refinement step | Cycle: 1 / Resolution: 1.5→47.78 Å
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Refine LS restraints |
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