2PCL

Crystal structure of ABC transporter with complex (aq_297) from aquifex aeolicus VF5

• PDB DOI: https://doi.org/10.2210/pdb2PCL/pdb

• Classification: HYDROLASE
• Organism(s): Aquifex aeolicus VF5
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-03-30 Released: 2007-10-02 
• Deposition Author(s): Jeyakanthan, J., Kanaujia, S.P., Rafi, Z.A., Sekar, K., Ebihara, A., Nakagawa, N., Kuramitsu, S., Shinkai, A., Shiro, Y., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.247 
• R-Value Work: 0.201 
• R-Value Observed: 0.203 

Literature

Crystal structure of ABC transporter with complex (aq_297) from aquifex aeolicus VF5

Jeyakanthan, J., Kanaujia, S.P., Rafi, Z.A., Sekar, K., Nakagawa, N., Ebihara, A., Kuramitsu, S., Shinkai, A., Shiro, Y., Yokoyama, S.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 25.83 kDa 
• Atom Count: 2,121 
• Modelled Residue Count: 223 
• Deposited Residue Count: 224 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipoprotein-releasing system ATP-binding protein lolD	A	224	Aquifex aeolicus VF5	Mutation(s): 0  EC: 3.6.3
UniProt
Find proteins for O66646 (Aquifex aeolicus (strain VF5)) Explore O66646  Go to UniProtKB:  O66646

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	I [auth A], J [auth A], K [auth A], L [auth A], M [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.247 
• R-Value Work: 0.201 
• R-Value Observed: 0.203 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.177	α = 90
b = 104.177	β = 90
c = 135.046	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-10-02 
Deposition Author(s): Jeyakanthan, J., Kanaujia, S.P., Rafi, Z.A., Sekar, K., Ebihara, A., Nakagawa, N., Kuramitsu, S., Shinkai, A., Shiro, Y., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-10-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Derived calculations, Source and taxonomy, Version format compliance
• Version 1.2: 2017-10-18
  Changes: Refinement description
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description