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Yorodumi- PDB-2y5c: Structure of human ferredoxin 2 (Fdx2)in complex with 2Fe2S cluster -
+Open data
-Basic information
Entry | Database: PDB / ID: 2y5c | ||||||
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Title | Structure of human ferredoxin 2 (Fdx2)in complex with 2Fe2S cluster | ||||||
Components | ADRENODOXIN-LIKE PROTEIN, MITOCHONDRIAL | ||||||
Keywords | ELECTRON TRANSPORT / IRON-SULFUR CLUSTER BIOGENESIS | ||||||
Function / homology | Function and homology information Electron transport from NADPH to Ferredoxin / Defective CYP11A1 causes AICSR / small molecule metabolic process / Mitochondrial iron-sulfur cluster biogenesis / sterol metabolic process / C21-steroid hormone biosynthetic process / Pregnenolone biosynthesis / Endogenous sterols / 2 iron, 2 sulfur cluster binding / electron transfer activity ...Electron transport from NADPH to Ferredoxin / Defective CYP11A1 causes AICSR / small molecule metabolic process / Mitochondrial iron-sulfur cluster biogenesis / sterol metabolic process / C21-steroid hormone biosynthetic process / Pregnenolone biosynthesis / Endogenous sterols / 2 iron, 2 sulfur cluster binding / electron transfer activity / mitochondrial matrix / metal ion binding Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å | ||||||
Authors | Webert, H. / Hobler, A. / Sheftel, A.D. / Molik, S. / Maestre-Reyna, M. / Essen, L.-O. / Vorniscescu, D. / Keusgen, M. / Hannemann, F. / Bernhardt, R. / Lill, R. | ||||||
Citation | Journal: To be Published Title: Structure and Functional Studies on Human Mitochondrial Ferredoxins Authors: Webert, H. / Hobler, A. / Sheftel, A.D. / Molik, S. / Maestre-Reyna, M. / Essen, L.-O. / Vorniscescu, D. / Keusgen, M. / Hannemann, F. / Bernhardt, R. / Lill, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2y5c.cif.gz | 104 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2y5c.ent.gz | 81.4 KB | Display | PDB format |
PDBx/mmJSON format | 2y5c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y5/2y5c ftp://data.pdbj.org/pub/pdb/validation_reports/y5/2y5c | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 11949.489 Da / Num. of mol.: 2 / Fragment: RESIDUES 66-171 Source method: isolated from a genetically manipulated source Details: HOLOFORM WITH 2FE2S CLUSTER / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PASKIBA43PLUS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6P4F2 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | UNIPROT RESIDUES 1-52 ARE A MITOCHONDR | |
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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: 2.79 Å3/Da / Density % sol: 55.91 % / Description: NONE |
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Crystal grow | Details: 1.6 M SODIUM CITRATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.319 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 19, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.319 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→49.6 Å / Num. obs: 27945 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 17.958 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 22 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 5.2 / % possible all: 96.5 |
-Processing
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 1.7→49.6 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.978 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.148 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→49.6 Å
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