2FDR

Crystal Structure of Conserved Haloacid Dehalogenase-like Protein of Unknown Function ATU0790 from Agrobacterium tumefaciens str. C58

• PDB DOI: https://doi.org/10.2210/pdb2FDR/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Agrobacterium fabrum str. C58
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2005-12-14 Released: 2006-01-31 
• Deposition Author(s): Nocek, B., Xu, X., Zheng, H., Savchenko, A., Edwards, 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: 
  0.227 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.176 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Literature

Crystal structure of hydrolases/phosphatases-like fold protein from Agrobacterium tumefaciens str. C58

Nocek, B., Xu, X., Zheng, H., Savchenko, A., Edwards, A., Joachimiak, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 25.38 kDa 
• Atom Count: 1,872 
• Modelled Residue Count: 222 
• Deposited Residue Count: 229 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
conserved hypothetical protein	A	229	Agrobacterium fabrum str. C58	Mutation(s): 9
UniProt
Find proteins for A9CJW3 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore A9CJW3  Go to UniProtKB:  A9CJW3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-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:  0.227 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.176 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.237	α = 90
b = 48.179	β = 90
c = 104.42	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data scaling
HKL-3000	phasing
SHELXD	phasing
SOLVE	phasing
RESOLVE	phasing
MLPHARE	phasing
DM	phasing
ARP/wARP	model building
CCP4	phasing
SHELXE	model building
O	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-01-31 
Deposition Author(s): Nocek, B., Xu, X., Zheng, H., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2006-01-31
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary