3IQ0 | pdb_00003iq0

Crystal structure of a putative Ribokinase II in complex with ATP and Mg+2 from E.coli

• PDB DOI: https://doi.org/10.2210/pdb3IQ0/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli O6
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-08-18 Released: 2009-09-08 
• Deposition Author(s): Satyanarayana, L., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 
  0.255 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.228 (Depositor), 0.227 (DCC) 
• R-Value Observed: 
  0.228 (Depositor) 

Literature

Crystal structure of a putative Ribokinase (II)in complex with ATP and Mg+2 from E.coli

Satyanarayana, L., Burley, S.K., Swaminathan, S.

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: 74.19 kDa 
• Atom Count: 5,028 
• Modeled Residue Count: 615 
• Deposited Residue Count: 660 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative Ribokinase II	A, B	330	Escherichia coli O6	Mutation(s): 0  Gene Names: 1040397, c4014 EC: 2.7.1
UniProt
Find proteins for A0A0H2VDX9 (Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)) Explore A0A0H2VDX9  Go to UniProtKB:  A0A0H2VDX9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	D [auth A], G [auth B]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
MG	C [auth A], E [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-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: 1.79 Å
• R-Value Free:  0.255 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.228 (Depositor), 0.227 (DCC) 
• R-Value Observed: 0.228 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.304	α = 90
b = 87.256	β = 90
c = 112.249	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
SHELXCD	phasing
SHARP	phasing
CNS	refinement
DENZO	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-08 
Deposition Author(s): Satyanarayana, L., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2009-09-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Structure summary