3FD3 | pdb_00003fd3

Structure of the C-terminal domains of a LysR family protein from Agrobacterium tumefaciens str. C58.

• PDB DOI: https://doi.org/10.2210/pdb3FD3/pdb

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


• Deposited: 2008-11-24 Released: 2009-02-03 
• Deposition Author(s): Cuff, M.E., Xu, X., Zeng, H., Edwards, A., Savchenko, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.200 (Depositor), 0.209 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.178 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Literature

Structure of the C-terminal domains of a LysR family protein from Agrobacterium tumefaciens str. C58.

Cuff, M.E., Xu, X., Zeng, H., Edwards, A., Savchenko, A., Joachimiak, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 23.23 kDa 
• Atom Count: 2,003 
• Modeled Residue Count: 207 
• Deposited Residue Count: 208 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
chromosome replication initiation inhibitor protein	A	208	Agrobacterium fabrum str. C58	Mutation(s): 0  Gene Names: AGR_C_1691, Atu0928, oriC
UniProt
Find proteins for A9CJQ0 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore A9CJQ0  Go to UniProtKB:  A9CJQ0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P33	C [auth A]	3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL C14 H30 O8 XPJRQAIZZQMSCM-UHFFFAOYSA-N
PG4	D [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
EDO	E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-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: 1.70 Å
• R-Value Free:  0.200 (Depositor), 0.209 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.178 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.613	α = 90
b = 53.613	β = 90
c = 188.027	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-02-03 
Deposition Author(s): Cuff, M.E., Xu, X., Zeng, H., Edwards, A., Savchenko, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2009-02-03
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Source and taxonomy, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.4: 2024-10-30
  Changes: Structure summary