3WO5 | pdb_00003wo5

Crystal structure of S147Q of Rv2613c from Mycobacterium tuberculosis

• PDB DOI: https://doi.org/10.2210/pdb3WO5/pdb

• Classification: TRANSFERASE
• Organism(s): Mycobacterium tuberculosis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-12-20 Released: 2014-12-24 
• Deposition Author(s): Mori, S., Wachino, J., Arakawa, Y., Shibayama, K.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.79 Å
• R-Value Free: 
  0.235 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.172 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Starting Model: experimental

Literature

Role of Ser-147 and Ala-149 in catalytic activity of diadenosine tetraphosphate phosphorylase from Mycobacterium tuberculosis H37Rv

Mori, S., Wachino, J., Kim, H., Rimbara, E., Arakawa, Y., Shibayama, K.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 50.33 kDa 
• Atom Count: 2,771 
• Modeled Residue Count: 333 
• Deposited Residue Count: 436 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AP-4-A phosphorylase	A, B	218	Mycobacterium tuberculosis	Mutation(s): 1  Gene Names: MT2688, Rv2613c EC: 2.7.7.53
UniProt
Find proteins for P9WMK9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WMK9  Go to UniProtKB:  P9WMK9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	D [auth A], G [auth B]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PO4	C [auth A], E [auth B], F [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	H [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.79 Å
• R-Value Free:  0.235 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.172 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.015	α = 90
b = 63.55	β = 111.01
c = 79.025	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-24 
Deposition Author(s): Mori, S., Wachino, J., Arakawa, Y., Shibayama, K.

Revision History  

• Version 1.0: 2014-12-24
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description