3EAF | pdb_00003eaf

Crystal structure of ABC transporter, substrate binding protein Aeropyrum pernix

• PDB DOI: https://doi.org/10.2210/pdb3EAF/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Aeropyrum pernix
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-08-25 Released: 2008-09-09 
• Deposition Author(s): Zhang, Z., Eswaramoorthy, S., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.207 (Depositor), 0.209 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.167 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Literature

Crystal structure of ABC transporter, substrate binding protein Aeropyrum pernix

Zhang, Z., Eswaramoorthy, S., Burley, S.K., Swaminathan, S.

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: 43.53 kDa 
• Atom Count: 3,198 
• Modeled Residue Count: 384 
• Deposited Residue Count: 391 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ABC transporter, substrate binding protein	A	391	Aeropyrum pernix	Mutation(s): 0  Gene Names: APE1303, APE_1303.1
UniProt
Find proteins for Q9YCF4 (Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)) Explore Q9YCF4  Go to UniProtKB:  Q9YCF4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-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: 2.00 Å
• R-Value Free:  0.207 (Depositor), 0.209 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.167 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.125	α = 90
b = 91.07	β = 90
c = 192.86	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
SHELX	model building
SHARP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-09-09 
Deposition Author(s): Zhang, Z., Eswaramoorthy, S., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2008-09-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2024-11-06
  Changes: Data collection, Database references, Structure summary