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Yorodumi- PDB-6g7m: Four-site variant (Y222C, C197S, C432S, C433S) of E. coli hydroge... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6g7m | ||||||
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Title | Four-site variant (Y222C, C197S, C432S, C433S) of E. coli hydrogenase-2 | ||||||
Components | (Hydrogenase-2 ...) x 2 | ||||||
Keywords | OXIDOREDUCTASE / [NiFe]-Hydrogenase / hydrogen production / FeS clusters / nanoclusters | ||||||
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 / iron-sulfur cluster binding / nickel cation binding / 4 iron, 4 sulfur cluster binding ...hydrogenase (acceptor) / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase complex / hydrogenase (acceptor) activity / ferredoxin hydrogenase activity / anaerobic respiration / 3 iron, 4 sulfur cluster binding / iron-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 | Escherichia coli K12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å | ||||||
Authors | Carr, S.B. / Armstrong, F.A. / Zhang, L. / Beaton, S.E. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Energy Environ Sci / Year: 2019 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 | 6g7m.cif.gz | 352.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6g7m.ent.gz | 277.9 KB | Display | PDB format |
PDBx/mmJSON format | 6g7m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6g7m_validation.pdf.gz | 494.4 KB | Display | wwPDB validaton report |
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Full document | 6g7m_full_validation.pdf.gz | 498.1 KB | Display | |
Data in XML | 6g7m_validation.xml.gz | 62.3 KB | Display | |
Data in CIF | 6g7m_validation.cif.gz | 92.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g7/6g7m ftp://data.pdbj.org/pub/pdb/validation_reports/g7/6g7m | HTTPS FTP |
-Related structure data
Related structure data | 6eqhS 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
-Hydrogenase-2 ... , 2 types, 4 molecules STLM
#1: Protein | Mass: 32985.164 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Variant Y222C with C-terminal his-tag / Source: (natural) Escherichia coli K12 (bacteria) / References: UniProt: P69741, hydrogenase (acceptor) #2: Protein | Mass: 62509.719 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Triple variant C197S, C432S, C433S / Source: (natural) Escherichia coli K12 (bacteria) / References: UniProt: P0ACE0, hydrogenase (acceptor) |
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-Non-polymers , 6 types, 946 molecules
#3: Chemical | ChemComp-SF4 / #4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-MG / #8: 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: 2.14 Å3/Da / Density % sol: 42.6 % / Description: Long rectangular rods |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop / pH: 5.9 Details: 100 mM bis-tris pH 5.9, 200 mM MgCl2, 19-21 % PEG 3350 PH range: 5.5-5.9 / Temp details: ambient temperature in anaerobic glove box |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: Maintained with cryostream |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 16, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9159 Å / Relative weight: 1 |
Reflection | Resolution: 1.71→100 Å / Num. obs: 185232 / % possible obs: 100 % / Redundancy: 7.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.036 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 1.71→1.74 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.84 / Num. unique obs: 67425 / CC1/2: 0.819 / Rpim(I) all: 0.33 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6EQH Resolution: 1.71→86.75 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.977 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.318 Å2
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Refinement step | Cycle: 1 / Resolution: 1.71→86.75 Å
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Refine LS restraints |
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