+Open data
-Basic information
Entry | Database: PDB / ID: 5lry | ||||||
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Title | E coli [NiFe] Hydrogenase Hyd-1 mutant E28D | ||||||
Components | (Hydrogenase-1 ...) x 2 | ||||||
Keywords | OXIDOREDUCTASE / [NiFe]-Hydrogenase Hydrogen splitting Oxidoreductase | ||||||
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 / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli O6:H1 (bacteria) Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Carr, S.B. / Phillips, S.E.V. / Evans, R.M. / Brooke, E.J. / Armstrong, F.A. | ||||||
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 | 5lry.cif.gz | 678.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lry.ent.gz | 550.1 KB | Display | PDB format |
PDBx/mmJSON format | 5lry.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lr/5lry ftp://data.pdbj.org/pub/pdb/validation_reports/lr/5lry | HTTPS FTP |
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-Related structure data
Related structure data | 6fpiC 6fpoC 6fpwC 6g7rC 6galC 6gamC 6ganC 4uscS 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: 36814.676 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC) (bacteria) Variant: MC4100 / Strain: CFT073 / ATCC 700928 / UPEC / References: UniProt: P69740, hydrogenase (acceptor) #2: Protein | Mass: 64769.363 Da / Num. of mol.: 2 / Mutation: E28D / Source method: isolated from a natural source Details: Cys 576 shos oxidation damage and is modelled as sulfinic acid (csd). Mutatiojn E28D introduced to test function of variant protein. Source: (natural) Escherichia coli (strain K12) (bacteria) / Variant: MC4100 / Strain: K12 / References: UniProt: P0ACD8, hydrogenase (acceptor) |
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-Sugars , 1 types, 2 molecules
#6: Sugar |
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-Non-polymers , 10 types, 1446 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #7: Chemical | #8: Chemical | #9: Chemical | #10: Chemical | #11: Chemical | #12: Chemical | ChemComp-LI / | #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: 2.31 Å3/Da / Density % sol: 46.84 % / Description: Highly elongated rods |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.1 Details: 100 mM Tris pH 8.1, 20-24 % PEG 3350 200 mM LiSO4 150 mM NaCl PH range: 8.0-8.3 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 25, 2016 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→99 Å / Num. obs: 337237 / % possible obs: 99.4 % / Redundancy: 6.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.136 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 1.4→1.42 Å / Redundancy: 6.4 % / Rmerge(I) obs: 1.453 / Mean I/σ(I) obs: 1.4 / CC1/2: 0.515 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb 4usc Resolution: 1.4→92.79 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.968 / SU B: 2.169 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.05 / ESU R Free: 0.051 / 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: 12.771 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→92.79 Å
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