3C9H | pdb_00003c9h

Crystal structure of the substrate binding protein of the ABC transporter from Agrobacterium tumefaciens

• PDB DOI: https://doi.org/10.2210/pdb3C9H/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Agrobacterium fabrum str. C58
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2008-02-15 Released: 2008-03-04 
• Deposition Author(s): Zhang, R., Xu, X., Zheng, H., Savchenko, A., Edwards, A.M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.228 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Literature

The crystal structure of the substrate binding protein of the ABC transporter from Agrobacterium tumefaciens.

Zhang, R., Xu, X., Zheng, H., Savchenko, A., Edwards, A.M., Joachimiak, A.

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 79.36 kDa 
• Atom Count: 5,726 
• Modeled Residue Count: 673 
• Deposited Residue Count: 710 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ABC transporter, substrate binding protein	A, B	355	Agrobacterium fabrum str. C58	Mutation(s): 0  Gene Names: GI:17936349, AGR_C_4480, Atu2467
UniProt
Find proteins for Q7CWZ6 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore Q7CWZ6  Go to UniProtKB:  Q7CWZ6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	D [auth A], F [auth B]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
MG	C [auth A], E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.228 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.313	α = 90
b = 86.947	β = 90
c = 109.642	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
MLPHARE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-03-04 
Deposition Author(s): Zhang, R., Xu, X., Zheng, H., Savchenko, A., Edwards, A.M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2008-03-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations