+Open data
-Basic information
Entry | Database: PDB / ID: 6jo2 | |||||||||
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Title | Ferredoxin I from Thermosynechococcus elongatus | |||||||||
Components | Ferredoxin-1 | |||||||||
Keywords | ELECTRON TRANSPORT / Photosynthesis | |||||||||
Function / homology | Function and homology information electron transport chain / 2 iron, 2 sulfur cluster binding / electron transfer activity / metal ion binding Similarity search - Function | |||||||||
Biological species | Thermosynechococcus elongatus BP-1 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 Å | |||||||||
Authors | Motomura, T. | |||||||||
Citation | Journal: Biochim Biophys Acta Bioenerg / Year: 2019 Title: An alternative plant-like cyanobacterial ferredoxin with unprecedented structural and functional properties. Authors: Motomura, T. / Zuccarello, L. / Setif, P. / Boussac, A. / Umena, Y. / Lemaire, D. / Tripathy, J.N. / Sugiura, M. / Hienerwadel, R. / Shen, J.R. / Berthomieu, C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6jo2.cif.gz | 61.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jo2.ent.gz | 44.2 KB | Display | PDB format |
PDBx/mmJSON format | 6jo2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6jo2_validation.pdf.gz | 434.8 KB | Display | wwPDB validaton report |
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Full document | 6jo2_full_validation.pdf.gz | 434.7 KB | Display | |
Data in XML | 6jo2_validation.xml.gz | 7.2 KB | Display | |
Data in CIF | 6jo2_validation.cif.gz | 9.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jo/6jo2 ftp://data.pdbj.org/pub/pdb/validation_reports/jo/6jo2 | HTTPS FTP |
-Related structure data
Related structure data | 6iriC 5auiS 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
#1: Protein | Mass: 10722.764 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermosynechococcus elongatus BP-1 (bacteria) Gene: petF1, petF, tsl1009 Production host: Thermosynechococcus elongatus BP-1 (bacteria) References: UniProt: P0A3C9 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-FES / | #4: Chemical | ChemComp-SO4 / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 100 mM Sodium Citrate (pH 6.5) 2.5 M ammonium Sulfate 0.2%(w/v) benzamidine hydrochloride 3%(w/v) 1,6-hexanediol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 9, 2019 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.55→38.61 Å / Num. obs: 13408 / % possible obs: 96.5 % / Redundancy: 3.3 % / Net I/σ(I): 12.04 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5AUI Resolution: 1.55→38.61 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.957 / WRfactor Rfree: 0.1783 / WRfactor Rwork: 0.1339 / FOM work R set: 0.8757 / SU B: 3.321 / SU ML: 0.053 / SU R Cruickshank DPI: 0.1031 / SU Rfree: 0.0771 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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 max: 54.46 Å2 / Biso mean: 14.938 Å2 / Biso min: 4.26 Å2
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Refinement step | Cycle: final / Resolution: 1.55→38.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.548→1.588 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -15.912 Å / Origin y: -0.1129 Å / Origin z: 1.8159 Å
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