- PDB-2y5c: Structure of human ferredoxin 2 (Fdx2)in complex with 2Fe2S cluster -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 2y5c
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
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
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Processing
Software
Name
Version
Classification
REFMAC
5.5.0102
refinement
XDS
datareduction
SCALA
datascaling
SHELXCDE
phasing
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.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.20051
765
2.7 %
RANDOM
Rwork
0.17281
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obs
0.17356
27945
97.93 %
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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