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Yorodumi- PDB-6gal: Structure of fully reduced Hydrogenase (Hyd-1) variant E28Q colle... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6gal | ||||||
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Title | Structure of fully reduced Hydrogenase (Hyd-1) variant E28Q collected at pH 10 | ||||||
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) Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 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 | 6gal.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6gal.ent.gz | 1 MB | Display | PDB format |
PDBx/mmJSON format | 6gal.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ga/6gal ftp://data.pdbj.org/pub/pdb/validation_reports/ga/6gal | HTTPS FTP |
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-Related structure data
Related structure data | 5lryC 6fpiC 6fpoC 6fpwC 6g7rC 6gamC 6ganC 5lmmS 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
-Hydrogenase-1 ... , 2 types, 4 molecules STLM
#1: Protein | Mass: 36814.676 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Two additional amino acids visible at N-terminus relative to chain S Source: (gene. exp.) Escherichia coli K-12 (bacteria) Description: chromosomal copy of the HybA gene has been engineered to add a his-tag Gene: hyaA, b0972, JW0954 / Production host: Escherichia coli (E. coli) / 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 (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0ACD8, hydrogenase (acceptor) |
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-Non-polymers , 10 types, 1397 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | #8: Chemical | #9: Chemical | #10: Chemical | ChemComp-CXS / | #11: Chemical | #12: 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: 2.08 Å3/Da / Density % sol: 40.8 % / Description: Long rods with rectangular cross section |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop / pH: 8.1 Details: 100 mM tris pH 8.1, 200 mm LiSO4 150 mM NaCl 19-21% PEG 3350 PH range: 8.0-8.2 / Temp details: Ambient temperature in 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: I24 / Wavelength: 0.9686 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 2, 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: 1.25→95 Å / Num. obs: 437084 / % possible obs: 95.9 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 1.25→1.32 Å / Rmerge(I) obs: 0.96 / Mean I/σ(I) obs: 1.8 / % possible all: 93.1 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5LMM Resolution: 1.25→92.12 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.975 / SU B: 1.386 / SU ML: 0.026 / Cross valid method: THROUGHOUT / ESU R: 0.036 / ESU R Free: 0.036 / 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: 11.36 Å2
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Refinement step | Cycle: LAST / Resolution: 1.25→92.12 Å
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