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Yorodumi- PDB-8bj7: Desulfovibrio desulfuricans FeFe Hydrogenase C178A mutant in Hina... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8bj7 | ||||||
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Title | Desulfovibrio desulfuricans FeFe Hydrogenase C178A mutant in Hinact-like state | ||||||
Components |
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Keywords | OXIDOREDUCTASE / [FeFe] Hydrogenase / C178A mutant | ||||||
Function / homology | Function and homology information ferredoxin hydrogenase / ferredoxin hydrogenase activity / iron-sulfur cluster binding / 4 iron, 4 sulfur cluster binding / periplasmic space / electron transfer activity / iron ion binding Similarity search - Function | ||||||
Biological species | Desulfovibrio desulfuricans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.04 Å | ||||||
Authors | Bikbaev, K. / Span, I. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Chem Sci / Year: 2023 Title: Binding of exogenous cyanide reveals new active-site states in [FeFe] hydrogenases. Authors: Martini, M.A. / Bikbaev, K. / Pang, Y. / Lorent, C. / Wiemann, C. / Breuer, N. / Zebger, I. / DeBeer, S. / Span, I. / Bjornsson, R. / Birrell, J.A. / Rodriguez-Macia, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8bj7.cif.gz | 208.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bj7.ent.gz | 159.3 KB | Display | PDB format |
PDBx/mmJSON format | 8bj7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8bj7_validation.pdf.gz | 2.4 MB | Display | wwPDB validaton report |
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Full document | 8bj7_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 8bj7_validation.xml.gz | 24.4 KB | Display | |
Data in CIF | 8bj7_validation.cif.gz | 36.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bj/8bj7 ftp://data.pdbj.org/pub/pdb/validation_reports/bj/8bj7 | HTTPS FTP |
-Related structure data
Related structure data | 8bj8C 6sg2S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 43191.699 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desulfovibrio desulfuricans (bacteria) Strain: ATCC 29579 / DSM 644 / NCIMB 8303 / VKM B-1760 / Hildenborough Gene: hydA, DVU_1769 / Production host: Escherichia coli (E. coli) / References: UniProt: P07598, ferredoxin hydrogenase | ||||||
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#2: Protein | Mass: 10082.425 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desulfovibrio desulfuricans (bacteria) Strain: ATCC 29579 / DSM 644 / NCIMB 8303 / VKM B-1760 / Hildenborough Gene: hydB, DVU_1770 / Production host: Escherichia coli (E. coli) / References: UniProt: P07603, ferredoxin hydrogenase | ||||||
#3: Chemical | #4: Chemical | ChemComp-VHR / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.8 Å3/Da / Density % sol: 31.54 % |
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Crystal grow | Temperature: 281.15 K / Method: vapor diffusion, sitting drop / pH: 7.6 Details: 1 M Lithium chloride, 0.1 M Sodium acetate, 30 % Polyethylene glycol 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.8266 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 19, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8266 Å / Relative weight: 1 |
Reflection | Resolution: 1.04→44.528 Å / Num. obs: 183605 / % possible obs: 99.7 % / Redundancy: 13 % / CC1/2: 0.999 / Rmerge(I) obs: 0.119 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 1.04→1.06 Å / Rmerge(I) obs: 2.447 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 8992 / CC1/2: 0.499 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6SG2 Resolution: 1.04→44.528 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.978 / SU B: 0.452 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R: 0.027 / ESU R Free: 0.028 Details: Hydrogens have been added in their 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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.42 Å2
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Refinement step | Cycle: LAST / Resolution: 1.04→44.528 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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