3DXO | pdb_00003dxo

CRYSTAL STRUCTURE OF A PUTATIVE ISOMERASE OF THE SNOAL-LIKE FAMILY (ATU_0744) FROM AGROBACTERIUM TUMEFACIENS STR. C58 AT 2.70 A RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb3DXO/pdb

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


• Deposited: 2008-07-24 Released: 2008-08-12 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.262 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.231 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.233 (Depositor) 

Literature

Crystal structure of SnoaL-like Protein with Unknown Function (17739112) from AGROBACTERIUM TUMEFACIENS str. C58 (Dupont) at 2.70 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 27.44 kDa 
• Atom Count: 1,927 
• Modeled Residue Count: 235 
• Deposited Residue Count: 242 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
uncharacterized SnoaL-like Protein	A, B	121	Agrobacterium fabrum str. C58	Mutation(s): 0  Gene Names: 17739112, AGR_C_1349, Atu0744
UniProt
Find proteins for Q7D0S4 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore Q7D0S4  Go to UniProtKB:  Q7D0S4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE	C [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG	D [auth A], E [auth B], F [auth B], G [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.262 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.231 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.233 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33DXO

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.57	α = 90
b = 119.57	β = 90
c = 94.49	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-08-12 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2008-08-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2020-09-09
  Changes: Derived calculations, Refinement description
• Version 1.5: 2023-02-01
  Changes: Database references
• Version 1.6: 2024-11-20
  Changes: Data collection, Refinement description, Structure summary