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Yorodumi- PDB-4c3o: Structure and function of an oxygen tolerant NiFe hydrogenase fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4c3o | |||||||||
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Title | Structure and function of an oxygen tolerant NiFe hydrogenase from Salmonella | |||||||||
Components | (HYDROGENASE-1 ...) x 2 | |||||||||
Keywords | OXIDOREDUCTASE / HYDROGEN METABOLISM / NIFE HYDROGENASE | |||||||||
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 / periplasmic space ...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 / periplasmic space / electron transfer activity / membrane / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM STR. LT2 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | |||||||||
Authors | Bowman, L. / Flanagan, L. / Fyfe, P.K. / Parkin, A. / Hunter, W.N. / Sargent, F. | |||||||||
Citation | Journal: Biochem.J. / Year: 2014 Title: How the Structure of the Large Subunit Controls Function in an Oxygen-Tolerant [Nife]-Hydrogenase. Authors: Bowman, L. / Flanagan, L. / Fyfe, P.K. / Parkin, A. / Hunter, W.N. / Sargent, F. #1: Journal: FEBS Lett. / Year: 2012 Title: How Salmonella Oxidises H(2) Under Aerobic Conditions. Authors: Parkin, A. / Bowman, L. / Roessler, M.M. / Davies, R.A. / Palmer, T. / Armstrong, F.A. / Sargent, F. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4c3o.cif.gz | 1018 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4c3o.ent.gz | 849.8 KB | Display | PDB format |
PDBx/mmJSON format | 4c3o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4c3o_validation.pdf.gz | 548.7 KB | Display | wwPDB validaton report |
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Full document | 4c3o_full_validation.pdf.gz | 573.4 KB | Display | |
Data in XML | 4c3o_validation.xml.gz | 86.3 KB | Display | |
Data in CIF | 4c3o_validation.cif.gz | 117.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c3/4c3o ftp://data.pdbj.org/pub/pdb/validation_reports/c3/4c3o | HTTPS FTP |
-Related structure data
Related structure data | 3rgwS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
NCS oper:
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-Components
-HYDROGENASE-1 ... , 2 types, 6 molecules ACEBDF
#1: Protein | Mass: 65148.836 Da / Num. of mol.: 3 / Fragment: RESIDUES 1-585 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM STR. LT2 (bacteria) Variant: LT2A Production host: SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM (bacteria) References: UniProt: Q8ZPH0, ferredoxin hydrogenase #2: Protein | Mass: 30989.432 Da / Num. of mol.: 3 / Fragment: RESIDUES 46-314 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM STR. LT2 (bacteria) Variant: LT2A Production host: SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM (bacteria) References: UniProt: Q8ZPG9, ferredoxin hydrogenase |
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-Non-polymers , 8 types, 137 molecules
#3: Chemical | #4: Chemical | ChemComp-CL / #5: Chemical | #6: Chemical | #7: Chemical | #8: Chemical | #9: Chemical | #10: Water | ChemComp-HOH / | |
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-Details
Sequence details | 15 RESIDUES FROM C-TERMINUS OF LARGE SUBUNIT PROTEOLYTICALLY PROCESSED 54 RESIDUES FROM C-TERMINUS ...15 RESIDUES FROM C-TERMINUS OF LARGE SUBUNIT PROTEOLYTI |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.98 Å3/Da / Density % sol: 69.13 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 19, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→29.5 Å / Num. obs: 51795 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 83.8 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 3.2→3.38 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 1.8 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3RGW Resolution: 3.2→29.52 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.933 / SU B: 43.429 / SU ML: 0.328 / Cross valid method: THROUGHOUT / ESU R Free: 0.427 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
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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: 87.343 Å2
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Refinement step | Cycle: LAST / Resolution: 3.2→29.52 Å
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Refine LS restraints |
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