[English] 日本語
Yorodumi- PDB-5fs8: Crystal structure of the G308E mutant of human apoptosis inducing... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fs8 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the G308E mutant of human apoptosis inducing factor | ||||||
Components | APOPTOSIS-INDUCING FACTOR 1, MITOCHONDRIAL | ||||||
Keywords | OXIDOREDUCTASE / MITOCHONDRIA / FLAVOPROTEIN | ||||||
Function / homology | Function and homology information Oxidoreductases; Acting on NADH or NADPH; With unknown physiological acceptors / regulation of apoptotic DNA fragmentation / mitochondrial respiratory chain complex assembly / NAD(P)H oxidase H2O2-forming activity / poly-ADP-D-ribose binding / cellular response to aldosterone / positive regulation of necroptotic process / protein import into mitochondrial intermembrane space / chromosome condensation / oxidoreductase activity, acting on NAD(P)H ...Oxidoreductases; Acting on NADH or NADPH; With unknown physiological acceptors / regulation of apoptotic DNA fragmentation / mitochondrial respiratory chain complex assembly / NAD(P)H oxidase H2O2-forming activity / poly-ADP-D-ribose binding / cellular response to aldosterone / positive regulation of necroptotic process / protein import into mitochondrial intermembrane space / chromosome condensation / oxidoreductase activity, acting on NAD(P)H / response to L-glutamate / NADH dehydrogenase activity / mitochondrial respiratory chain complex I assembly / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / cellular response to nitric oxide / FAD binding / cellular response to estradiol stimulus / response to ischemia / neuron differentiation / mitochondrial intermembrane space / response to toxic substance / cellular response to hydrogen peroxide / activation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of neuron apoptotic process / cellular response to hypoxia / neuron apoptotic process / mitochondrial inner membrane / protein dimerization activity / positive regulation of apoptotic process / apoptotic process / perinuclear region of cytoplasm / mitochondrion / DNA binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Sevrioukova, I. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2016 Title: Structure/Function Relations in Aifm1 Variants Associated with Neurodegenerative Disorders Authors: Sevrioukova, I. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5fs8.cif.gz | 219.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5fs8.ent.gz | 174.1 KB | Display | PDB format |
PDBx/mmJSON format | 5fs8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fs8_validation.pdf.gz | 707.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5fs8_full_validation.pdf.gz | 715.4 KB | Display | |
Data in XML | 5fs8_validation.xml.gz | 26.9 KB | Display | |
Data in CIF | 5fs8_validation.cif.gz | 42 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fs/5fs8 ftp://data.pdbj.org/pub/pdb/validation_reports/fs/5fs8 | HTTPS FTP |
-Related structure data
Related structure data | 5fs6C 5fs7C 5fs9C 1m6iS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 56339.031 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 103-613 / Mutation: YES Source method: isolated from a genetically manipulated source Details: ADDITIONAL C-TERMINAL RESIDUES L614-V615-P616-R617 ARE PART OF THE THROMBIN SITE. RESIDUES 104-124,546-558 AND 612-617 ARE DISORDERED Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: O95831, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor |
---|---|
#2: Chemical | ChemComp-FAD / |
#3: Water | ChemComp-HOH / |
Sequence details | G308E MUTATION AND ADDITIONAL |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.75 % / Description: NONE |
---|---|
Crystal grow | pH: 7.5 Details: 0.2 M AMMONIUM ACETATE AND 20% POLY-ETHYLENE GLYCOL, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 110 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98 |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 7, 2012 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→37.17 Å / Num. obs: 102452 / % possible obs: 97.1 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 1.4→1.48 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 1.5 / % possible all: 88.7 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1M6I Resolution: 1.4→89.75 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.34 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.057 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 23.382 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→89.75 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|