2PPX | pdb_00002ppx

Crystal structure of a HTH XRE-family like protein from Agrobacterium tumefaciens

• PDB DOI: https://doi.org/10.2210/pdb2PPX/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Agrobacterium fabrum str. C58
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-04-30 Released: 2007-05-29 
• Deposition Author(s): Cuff, M.E., Skarina, T., Onopriyenko, O., Edwards, A., Savchenko, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.244 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Literature

Structure of a HTH XRE-family like protein from Agrobacterium tumefaciens.

Cuff, M.E., Skarina, T., Onopriyenko, O., Edwards, A., Savchenko, A., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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 generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 11.69 kDa 
• Atom Count: 647 
• Modeled Residue Count: 62 
• Deposited Residue Count: 99 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein Atu1735	A	99	Agrobacterium fabrum str. C58	Mutation(s): 2  Gene Names: Atu1735, AGR_C_3184
UniProt
Find proteins for A9CIQ1 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore A9CIQ1  Go to UniProtKB:  A9CIQ1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	H [auth A], I [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-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:  0.244 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.696	α = 90
b = 70.696	β = 90
c = 103.736	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building
CCP4	phasing
O	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-05-29 
Deposition Author(s): Cuff, M.E., Skarina, T., Onopriyenko, O., Edwards, A., Savchenko, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2007-05-29
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Derived calculations, Source and taxonomy, Version format compliance
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary