+Open data
-Basic information
Entry | Database: PDB / ID: 5jrd | ||||||
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Title | E. coli Hydrogenase-1 variant P508A | ||||||
Components | (Hydrogenase-1 ...) x 2 | ||||||
Keywords | OXIDOREDUCTASE / Hydrogen activation / NiFe Hydrogenase | ||||||
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 O6:H1 (bacteria) Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||
Authors | Carr, S.B. / Phillips, S.E.V. / Armstrong, F.A. / Evans, R.M. / Brooke, E.J. / Islam, S.T.A. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Biochemistry / Year: 2017 Title: Importance of the Active Site "Canopy" Residues in an O2-Tolerant [NiFe]-Hydrogenase. Authors: Brooke, E.J. / Evans, R.M. / Islam, S.T. / Roberts, G.M. / Wehlin, S.A. / Carr, S.B. / Phillips, S.E. / 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 | 5jrd.cif.gz | 737.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jrd.ent.gz | 598.2 KB | Display | PDB format |
PDBx/mmJSON format | 5jrd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5jrd_validation.pdf.gz | 524.8 KB | Display | wwPDB validaton report |
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Full document | 5jrd_full_validation.pdf.gz | 535.2 KB | Display | |
Data in XML | 5jrd_validation.xml.gz | 71.6 KB | Display | |
Data in CIF | 5jrd_validation.cif.gz | 108.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jr/5jrd ftp://data.pdbj.org/pub/pdb/validation_reports/jr/5jrd | HTTPS FTP |
-Related structure data
Related structure data | 5a4mS 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: substrain MC4100 Source: (gene. exp.) Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC) (bacteria) Gene: hyaA, c1113 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P69740, hydrogenase (acceptor) #2: Protein | Mass: 64741.348 Da / Num. of mol.: 2 / Mutation: P508A Source method: isolated from a genetically manipulated source Details: substrain MC4100 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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-Non-polymers , 9 types, 1390 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-CL / #7: Chemical | #8: Chemical | #9: Chemical | #10: Chemical | #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: 2.28 Å3/Da / Density % sol: 46.1 % / Description: Rectangular rods |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: Peg 3350, 50 mM Bis-tris, 200 mM LiSO4, 150 mM NaCl PH range: 5.7-6.1 |
-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 2M / Detector: PIXEL / Date: Jul 4, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→98.6 Å / Num. obs: 536585 / % possible obs: 100 % / Redundancy: 7.2 % / CC1/2: 0.995 / Rmerge(I) obs: 0.13 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 1.2→1.22 Å / Redundancy: 7 % / Mean I/σ(I) obs: 1.6 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb 5a4m Resolution: 1.2→92.69 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.981 / SU B: 1.169 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R: 0.03 / ESU R Free: 0.029 / 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: 15.85 Å2
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Refinement step | Cycle: 1 / Resolution: 1.2→92.69 Å
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