4LII | pdb_00004lii

Crystal structure of an apoptosis-inducing factor, mitochondrion-associated, 1 (AIFM1) from Homo sapiens at 1.88 A resolution

• PDB DOI: https://doi.org/10.2210/pdb4LII/pdb

• Classification: OXIDOREDUCTASE, APOPTOSIS
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-07-02 Released: 2013-09-04 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG), Partnership for T-Cell Biology (TCELL)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free: 
  0.211 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.176 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Literature

Crystal structure of an apoptosis-inducing factor, mitochondrion-associated, 1 (AIFM1) from Homo sapiens at 1.88 A resolution

Joint Center for Structural Genomics (JCSG), Partnership for T-Cell Biology (TCELL)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 57.13 kDa 
• Atom Count: 4,082 
• Modeled Residue Count: 474 
• Deposited Residue Count: 513 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Apoptosis-inducing factor 1, mitochondrial	A	513	Homo sapiens	Mutation(s): 0  Gene Names: AIF, AIFM1, BC111065, PDCD8 EC: 1 (PDB Primary Data), 1.6.99 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O95831 (Homo sapiens) Explore O95831  Go to UniProtKB:  O95831
PHAROS:  O95831 GTEx:  ENSG00000156709

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	B [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
EDO	C [auth A], D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free:  0.211 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.176 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34LII

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.68	α = 90
b = 89.807	β = 94.78
c = 60.471	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
XSCALE	data scaling
REFMAC	refinement
XDS	data reduction
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-09-04 
Deposition Author(s): Joint Center for Structural Genomics (JCSG), Partnership for T-Cell Biology (TCELL)

Revision History  

• Version 1.0: 2013-09-04
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary