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Yorodumi- PDB-4iuc: Crystal structure of an O2-tolerant [NiFe]-hydrogenase from Ralst... -
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-Basic information
Entry | Database: PDB / ID: 4iuc | ||||||
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Title | Crystal structure of an O2-tolerant [NiFe]-hydrogenase from Ralstonia eutropha in its as-isolated form - oxidized state 2 | ||||||
Components | (Uptake hydrogenase ...) x 2 | ||||||
Keywords | 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 | 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 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Frielingsdorf, S. / Schmidt, A. / Fritsch, J. / Lenz, O. / Scheerer, P. | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2014 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4iuc.cif.gz | 403.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4iuc.ent.gz | 323.8 KB | Display | PDB format |
PDBx/mmJSON format | 4iuc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4iuc_validation.pdf.gz | 489.2 KB | Display | wwPDB validaton report |
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Full document | 4iuc_full_validation.pdf.gz | 491.6 KB | Display | |
Data in XML | 4iuc_validation.xml.gz | 41.8 KB | Display | |
Data in CIF | 4iuc_validation.cif.gz | 65.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iu/4iuc ftp://data.pdbj.org/pub/pdb/validation_reports/iu/4iuc | HTTPS FTP |
-Related structure data
Related structure data | 4iubC 4iudC 3rgwS C: citing same article (ref.) S: Starting model for refinement |
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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 / Fragment: UNP residues 1-603 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ralstonia eutropha (bacteria) / Strain: ATCC 17699 / H16 / DSM 428 / Stanier 337 / Gene: hoxG, PHG002 / Production host: Ralstonia eutropha (bacteria) 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.) Ralstonia eutropha (bacteria) / Strain: ATCC 17699 / H16 / DSM 428 / Stanier 337 / Gene: hoxK, PHG001 / Production host: Ralstonia eutropha (bacteria) Strain (production host): ATCC 17699 / H16 / DSM 428 / Stanier 337 References: UniProt: P31892, EC: 1.12.5.1 |
-Non-polymers , 7 types, 1053 molecules
#3: Chemical | ChemComp-NFV / | ||||||||
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#4: Chemical | ChemComp-MG / | ||||||||
#5: Chemical | #6: Chemical | ChemComp-SF4 / | #7: Chemical | ChemComp-F3S / | #8: Chemical | ChemComp-S3F / | #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: 39.49 % |
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Crystal grow | Temperature: 282 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 20-30% PEG3350, 100 mM Bis-Tris methane, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 282K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å |
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→34.36 Å / Num. obs: 150727 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 13.52 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 18 |
Reflection shell | Resolution: 1.45→1.53 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 2.7 / Num. unique all: 21390 / Rsym value: 0.496 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3RGW Resolution: 1.45→34.36 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.97 / 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: 14.215 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→34.36 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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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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