+Open data
-Basic information
Entry | Database: PDB / ID: 6rp2 | ||||||
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Title | Threonine to Cysteine (T225C) variant of E coli hydrogenase-1 | ||||||
Components | (Hydrogenase-1 ...) x 2 | ||||||
Keywords | OXIDOREDUCTASE / [NiFe]-Hydrogenase / hydrogen production / FeS clusters / nanoclusters | ||||||
Function / homology | Function and homology information hydrogen metabolic process / fermentation / hydrogenase (acceptor) / anaerobic electron transport chain / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase complex / hydrogenase (acceptor) activity / periplasmic side of plasma membrane / ferredoxin hydrogenase activity / anaerobic respiration ...hydrogen metabolic process / fermentation / hydrogenase (acceptor) / anaerobic electron transport chain / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase complex / hydrogenase (acceptor) activity / periplasmic side of plasma membrane / ferredoxin hydrogenase activity / anaerobic respiration / 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 / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli K-12 (bacteria) Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||
Authors | Carr, S.B. / Armstrong, F.A. / Zhang, L. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2020 Title: Aerobic Photocatalytic H2Production by a [NiFe] Hydrogenase Engineered to Place a Silver Nanocluster in the Electron Relay. Authors: Zhang, L. / Morello, G. / Carr, S.B. / Armstrong, F.A. #1: Journal: Energy Environ Sci / Year: 2018 Title: Direct visible light activation of a surface cysteine-engineered [NiFe]-hydrogenase by silver nanoclusters Authors: Zhang, L. / Beaton, S.E. / 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 | 6rp2.cif.gz | 389.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rp2.ent.gz | 316.9 KB | Display | PDB format |
PDBx/mmJSON format | 6rp2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rp/6rp2 ftp://data.pdbj.org/pub/pdb/validation_reports/rp/6rp2 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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: 35387.195 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: D8B36_14215 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P69740, UniProt: P69739*PLUS #2: Protein | Mass: 64767.387 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: hyaB, b0973, JW0955 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0ACD8, hydrogenase (acceptor) |
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-Sugars , 1 types, 2 molecules
#6: Sugar |
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-Non-polymers , 10 types, 1537 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #7: Chemical | #8: Chemical | #9: Chemical | #10: Chemical | #11: Chemical | #12: Chemical | #13: 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: 2.23 Å3/Da / Density % sol: 44.85 % / Description: Long rods with rectangular cross-section |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.9 Details: 100 mM Bis-tris pH 5.9 200 mM LiSO4 150 mM NaCl 18-21% PEG 3350 PH range: 5.5-5.9 Temp details: Ambient temperature inside anaerobic glove box |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 6, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→86.2 Å / Num. obs: 363874 / % possible obs: 99.6 % / Redundancy: 12.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.037 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 1.35→1.37 Å / Redundancy: 7.2 % / Rmerge(I) obs: 1.54 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 17400 / CC1/2: 0.4 / Rpim(I) all: 0.55 / % possible all: 96 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→86.07 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.973 / SU B: 0.849 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.045 / ESU R Free: 0.046 / 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: 13.837 Å2
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Refinement step | Cycle: LAST / Resolution: 1.35→86.07 Å
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Refine LS restraints |
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