+Open data
-Basic information
Entry | Database: PDB / ID: 5auk | ||||||
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Title | Crystal structure of the Ga-substituted Ferredoxin | ||||||
Components | Ferredoxin-1 | ||||||
Keywords | ELECTRON TRANSPORT / Analogue / electron transfer protein | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å | ||||||
Authors | Kurisu, G. / Muraki, N. / Taya, M. / Hase, T. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Biochemistry / Year: 2015 Title: X-ray Structure and Nuclear Magnetic Resonance Analysis of the Interaction Sites of the Ga-Substituted Cyanobacterial Ferredoxin Authors: Mutoh, R. / Muraki, N. / Shinmura, K. / Kubota-Kawai, H. / Lee, Y.H. / Nowaczyk, M.M. / Rogner, M. / Hase, T. / Ikegami, T. / Kurisu, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5auk.cif.gz | 54.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5auk.ent.gz | 37.8 KB | Display | PDB format |
PDBx/mmJSON format | 5auk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5auk_validation.pdf.gz | 469.5 KB | Display | wwPDB validaton report |
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Full document | 5auk_full_validation.pdf.gz | 469.9 KB | Display | |
Data in XML | 5auk_validation.xml.gz | 6.8 KB | Display | |
Data in CIF | 5auk_validation.cif.gz | 8.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/au/5auk ftp://data.pdbj.org/pub/pdb/validation_reports/au/5auk | HTTPS FTP |
-Related structure data
Related structure data | 5auiC 1offS 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: 10237.038 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria) Strain: PCC 6803 / Kazusa / Gene: petF, fed / Production host: Escherichia coli (E. coli) / References: UniProt: P27320 | ||||
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#2: Chemical | ChemComp-GAK / [ | ||||
#3: Chemical | #4: Chemical | ChemComp-BEN / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.57 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 3.4 M ammonium sulfate, 2% (w/v) benzamidine hydrochloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Feb 1, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.62→40 Å / Num. obs: 13883 / % possible obs: 96.6 % / Redundancy: 14.2 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 64.1 |
Reflection shell | Resolution: 1.62→1.65 Å / Redundancy: 14.5 % / Rmerge(I) obs: 0.333 / Mean I/σ(I) obs: 10.2 / % possible all: 91.1 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1OFF Resolution: 1.62→27.56 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.12 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.438 Å2
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Refinement step | Cycle: LAST / Resolution: 1.62→27.56 Å
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Refine LS restraints |
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