+Open data
-Basic information
Entry | Database: PDB / ID: 1off | ||||||
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Title | 2Fe-2S Ferredoxin from Synechocystis sp. PCC 6803 | ||||||
Components | FERREDOXIN I | ||||||
Keywords | ELECTRON TRANSPORT / FERREDOXIN / ELECTRON TRANSFER / IRON-SULPHUR / 2FE-2S / METAL-BINDING | ||||||
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 | SYNECHOCYSTIS SP. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Van Den heuvel, R.H.H. / Mattevi, A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 Title: The Active Conformation of Glutamate Synthase and its Binding to Ferredoxin Authors: Van Den Heuvel, R.H.H. / Svergun, D.I. / Petoukhov, M.V. / Coda, A. / Curti, B. / Ravasio, S. / Vanoni, M.A. / Mattevi, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1off.cif.gz | 32.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1off.ent.gz | 21.5 KB | Display | PDB format |
PDBx/mmJSON format | 1off.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1off_validation.pdf.gz | 426.6 KB | Display | wwPDB validaton report |
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Full document | 1off_full_validation.pdf.gz | 427.3 KB | Display | |
Data in XML | 1off_validation.xml.gz | 7.2 KB | Display | |
Data in CIF | 1off_validation.cif.gz | 9.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/of/1off ftp://data.pdbj.org/pub/pdb/validation_reports/of/1off | HTTPS FTP |
-Related structure data
Related structure data | 1ofdC 1ofeC 1czpS 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
#1: Protein | Mass: 10368.233 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SYNECHOCYSTIS SP. (bacteria) / Strain: PCC6803 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P27320 |
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#2: Chemical | ChemComp-FES / |
#3: Water | ChemComp-HOH / |
Compound details | FERREDOXINS ARE IRON-SULFUR PROTEINS THAT ARE INVOLVED IN THE TRANSFER OF ELECTRONS IN A WIDE ...FERREDOXIN |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 49 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.50 | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. obs: 8723 / % possible obs: 98.5 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.055 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.317 / % possible all: 97.2 |
Reflection | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 33.5 Å / Num. measured all: 161518 / Rmerge(I) obs: 0.055 |
Reflection shell | *PLUS % possible obs: 97.2 % / Rmerge(I) obs: 0.317 / Mean I/σ(I) obs: 7.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1CZP Resolution: 1.8→33.52 Å / SU B: 2.689 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.125
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Displacement parameters | Biso mean: 22.385 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→33.52 Å
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Refinement | *PLUS Highest resolution: 1.8 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.216 / Rfactor Rwork: 0.176 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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