3DCI | pdb_00003dci

The Structure of a putative arylesterase from Agrobacterium tumefaciens str. C58

• PDB DOI: https://doi.org/10.2210/pdb3DCI/pdb

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


• Deposited: 2008-06-03 Released: 2008-09-30 
• Deposition Author(s): Cuff, M.E., Xu, X., Zheng, H., Binkowski, T.A., 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: 
  0.184 (Depositor), 0.189 (DCC) 
• R-Value Work: 
  0.148 (Depositor), 0.156 (DCC) 
• R-Value Observed: 
  0.149 (Depositor) 

Literature

The Structure of a putative arylesterase from Agrobacterium tumefaciens str. C58

Cuff, M.E., Xu, X., Zheng, H., Binkowski, T.A., Edwards, A., Savchenko, A., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content 

• Total Structure Weight: 75.53 kDa 
• Atom Count: 5,138 
• Modeled Residue Count: 624 
• Deposited Residue Count: 696 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Arylesterase	A, B, C	232	Agrobacterium fabrum str. C58	Mutation(s): 0  Gene Names: AGR_L_2749, Atu3454
UniProt
Find proteins for A9CF87 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore A9CF87  Go to UniProtKB:  A9CF87

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACY	CA [auth C], M [auth A], V [auth B]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N
CL	AA [auth C], BA [auth C], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], W [auth C], X [auth C], Y [auth C], Z [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C	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:  0.184 (Depositor), 0.189 (DCC) 
• R-Value Work:  0.148 (Depositor), 0.156 (DCC) 
• R-Value Observed: 0.149 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.204	α = 90
b = 131.397	β = 90
c = 122.332	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: 2008-09-30 
Deposition Author(s): Cuff, M.E., Xu, X., Zheng, H., Binkowski, T.A., Edwards, A., Savchenko, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2008-09-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Structure summary