3T94

Crystal structure of 5'-deoxy-5'-methylthioadenosine phosphorylase (MTAP) II complexed with 5'-deoxy-5'-methylthioadenosine and sulfate

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history. 


Literature

A corrected space group for Sulfolobus sulfataricus 5'-deoxy-5'-methylthioadenosine phosphorylase II.

Zhang, Y., Zwart, P.H., Ealick, S.E.

(2012) Acta Crystallogr D Biol Crystallogr 68: 249-252

  • DOI: https://doi.org/10.1107/S0907444911051699
  • Primary Citation of Related Structures:  
    3T94

  • PubMed Abstract: 

    5'-deoxy-5'-methylthioadenosine phosphorylase (MTAP) catalyzes the phosphorolytic cleavage of 5'-deoxy-5'-methylthioadenosine (MTA), a byproduct of polyamine biosynthesis. The Sulfolobus sulfataricus genome encodes two MTAPs. SsMTAP I has broad substrate specifity, accepting guanosine, inosine, adenosine and MTA, while SsMTAP II is specific for MTA. SsMTAP I forms a donut-shaped hexamer, while SsMTAP II is a hexamer formed from trimers packed face to face. The structure of SsMTAP II was originally determined in space group P1 (PDB entry 2a8y) and showed R32 pseudosymmetry. Post-analysis using phenix.xtriage showed that the correct space group is C2. Here, the structure refined in space group C2 is reported and the factors that initially led to the incorrect space-group assignment are discussed.

    • Organizational Affiliation: 

    Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, USA.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
5'-methylthioadenosine phosphorylase (MtaP)
A, B, C, D, E
A, B, C, D, E, F
270Saccharolobus solfataricusMutation(s): 0 
EC: 2.4.2.28
UniProt
Find proteins for Q97W94 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Explore Q97W94 
Go to UniProtKB:  Q97W94
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ97W94
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MTA
Query on MTA
Download Ideal Coordinates CCD File 
G [auth A]
J [auth B]
N [auth C]
P [auth D]
S [auth E]
G [auth A],
J [auth B],
N [auth C],
P [auth D],
S [auth E],
V [auth F]
5'-DEOXY-5'-METHYLTHIOADENOSINE
C11 H15 N5 O3 S
WUUGFSXJNOTRMR-IOSLPCCCSA-N
SO4
Query on SO4
Download Ideal Coordinates CCD File 
H [auth A]
I [auth A]
K [auth B]
L [auth B]
M [auth B]
H [auth A],
I [auth A],
K [auth B],
L [auth B],
M [auth B],
O [auth C],
Q [auth D],
R [auth D],
T [auth E],
U [auth E],
W [auth F]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.16α = 90
b = 138.093β = 92.21
c = 96.56γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction
SCALAdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-08-24
    Type: Initial release
  • Version 1.1: 2012-02-29
    Changes: Database references
  • Version 1.2: 2012-03-28
    Changes: Database references
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-11-27
    Changes: Structure summary