3I4P | pdb_00003i4p

Crystal structure of AsnC family transcriptional regulator from Agrobacterium tumefaciens

• PDB DOI: https://doi.org/10.2210/pdb3I4P/pdb

• Classification: transcription regulator
• Organism(s): Agrobacterium fabrum str. C58
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-07-02 Released: 2009-07-28 
• Deposition Author(s): Cymborowski, M., Chruszcz, M., Luo, H., Xu, X., Savchenko, A., Edwards, A., Joachimiak, A., Minor, W., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.214 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.233 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Literature

Crystal structure of AsnC family transcriptional regulator from Agrobacterium tumefaciens

Cymborowski, M., Chruszcz, M., Luo, H., Xu, X., Savchenko, A., Edwards, A., Joachimiak, A., Minor, W.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

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

Macromolecule Content 

• Total Structure Weight: 19.33 kDa 
• Atom Count: 1,355 
• Modeled Residue Count: 153 
• Deposited Residue Count: 162 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator, AsnC family	A	162	Agrobacterium fabrum str. C58	Mutation(s): 0  Gene Names: AGR_C_3460, Atu1885
UniProt
Find proteins for A9CIH8 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore A9CIH8  Go to UniProtKB:  A9CIH8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	H [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA	F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	B [auth A], C [auth A], D [auth A], E [auth A], G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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: 2.30 Å
• R-Value Free:  0.214 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.233 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.833	α = 90
b = 141.833	β = 90
c = 50.283	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
HKL-2000	data reduction
HKL-3000	phasing
MLPHARE	phasing
DM	model building
SHELXD	phasing
RESOLVE	model building
ARP	model building
Coot	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing
SHELXE	model building
RESOLVE	phasing
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-07-28 
Deposition Author(s): Cymborowski, M., Chruszcz, M., Luo, H., Xu, X., Savchenko, A., Edwards, A., Joachimiak, A., Minor, W., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2009-07-28
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2022-04-13
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2024-10-16
  Changes: Data collection, Structure summary