+Open data
-Basic information
Entry | Database: PDB / ID: 6fpi | |||||||||
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Title | Structure of fully reduced Hydrogenase (Hyd-1) variant E28Q | |||||||||
Components | (Hydrogenase-1 ...) x 2 | |||||||||
Keywords | OXIDOREDUCTASE / NiFe hydrogenase / Iron sulphur cluster / periplasm / hydrogen | |||||||||
Function / homology | Function and homology information hydrogen metabolic process / [Ni-Fe] hydrogenase complex / fermentation / hydrogenase (acceptor) / anaerobic electron transport chain / ferredoxin hydrogenase complex / periplasmic side of plasma membrane / hydrogenase (acceptor) activity / anaerobic respiration / ferredoxin hydrogenase activity ...hydrogen metabolic process / [Ni-Fe] hydrogenase complex / fermentation / hydrogenase (acceptor) / anaerobic electron transport chain / ferredoxin hydrogenase complex / periplasmic side of plasma membrane / hydrogenase (acceptor) activity / anaerobic respiration / ferredoxin hydrogenase activity / 3 iron, 4 sulfur cluster binding / nickel cation binding / cellular response to starvation / outer membrane-bounded periplasmic space / 4 iron, 4 sulfur cluster binding / electron transfer activity / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Escherichia coli K-12 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | |||||||||
Authors | Carr, S.B. / Armstrong, F.A. / Evans, R.M. | |||||||||
Funding support | United Kingdom, 1items
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Citation | Journal: J. Am. Chem. Soc. / Year: 2018 Title: Mechanistic Exploitation of a Self-Repairing, Blocked Proton Transfer Pathway in an O2-Tolerant [NiFe]-Hydrogenase. Authors: Evans, R.M. / Ash, P.A. / Beaton, S.E. / Brooke, E.J. / Vincent, K.A. / Carr, S.B. / Armstrong, F.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fpi.cif.gz | 667.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fpi.ent.gz | 545.5 KB | Display | PDB format |
PDBx/mmJSON format | 6fpi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fp/6fpi ftp://data.pdbj.org/pub/pdb/validation_reports/fp/6fpi | HTTPS FTP |
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-Related structure data
Related structure data | 5lryC 6fpoC 6fpwC 6g7rC 6galC 6gamC 6ganC 5lmmS 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
-Hydrogenase-1 ... , 2 types, 4 molecules STLM
#1: Protein | Mass: 35741.531 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Variant: RME018 / References: UniProt: P69739, hydrogenase (acceptor) #2: Protein | Mass: 64750.402 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Variant E28Q / Source: (natural) Escherichia coli K-12 (bacteria) / Variant: RME018 / References: UniProt: P0ACD8, hydrogenase (acceptor) |
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-Sugars , 1 types, 2 molecules
#6: Sugar |
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-Non-polymers , 8 types, 1243 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #7: Chemical | ChemComp-CL / #8: Chemical | #9: Chemical | #10: Chemical | ChemComp-SO4 / | #11: Water | ChemComp-HOH / | |
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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: 2.1 Å3/Da / Density % sol: 41.46 % / Description: Rods with rectangular cross-section |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop / pH: 5.7 Details: 100 mM Bis-tris pH 5.5-5.9, 200 mM LiSO4, 150 mM NaCl 19-22% PEG 3350 PH range: 5.5-5.9 / Temp details: Ambient temperature in anaerobic chamber |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 13, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→83.51 Å / Num. obs: 263161 / % possible obs: 98.2 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1.57 / % possible all: 96.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5LMM Resolution: 1.5→83.51 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.657 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.063 / 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: 21.51 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→83.51 Å
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Refine LS restraints |
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