1VKI | pdb_00001vki

Crystal structure of a putative oligo-nucleotide binding protein (atu3699, agr_l_2275) from agrobacterium tumefaciens str. c58 at 1.60 A resolution

• PDB DOI: https://doi.org/10.2210/pdb1VKI/pdb

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


• Deposited: 2004-05-24 Released: 2004-06-08 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.185 (Depositor), 0.201 (DCC) 
• R-Value Work: 
  0.152 (Depositor), 0.167 (DCC) 
• R-Value Observed: 
  0.154 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of hypothetical protein (ATU3699) from Agrobacterium tumefaciens at 1.60 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: 40.66 kDa 
• Atom Count: 3,124 
• Modeled Residue Count: 331 
• Deposited Residue Count: 362 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HYPOTHETICAL PROTEIN ATU3699	A, B	181	Agrobacterium fabrum str. C58	Mutation(s): 0  Gene Names: ATU3699
UniProt
Find proteins for A9CFJ8 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore A9CFJ8  Go to UniProtKB:  A9CFJ8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], E [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	D [auth A], F [auth B], G [auth B], H [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.185 (Depositor), 0.201 (DCC) 
• R-Value Work:  0.152 (Depositor), 0.167 (DCC) 
• R-Value Observed: 0.154 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M31VKI

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.997	α = 90
b = 64.848	β = 100.92
c = 77.427	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-06-08 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2004-06-08
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.4: 2023-09-20
  Changes: Data collection, Refinement description