5VN4 | pdb_00005vn4

Crystal structure of adenine phosphoribosyl transferase from Trypanosoma brucei in complex with AMP, pyrophosphate, and ribose-5-phosphate

• PDB DOI: https://doi.org/10.2210/pdb5VN4/pdb

• Classification: TRANSFERASE
• Organism(s): Trypanosoma brucei brucei TREU927
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-04-28 Released: 2017-05-24 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 
  0.175 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.143 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.144 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of adenine phosphoribosyl transferase from Trypanosoma brucei in complex with AMP, pyrophosphate, and ribose-5-phosphate

Mayclin, S.J., Dranow, D.M., Lorimer, D.D., Edwards, T.E.

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: 55.18 kDa 
• Atom Count: 4,532 
• Modeled Residue Count: 468 
• Deposited Residue Count: 486 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenine phosphoribosyltransferase, putative	A, B	243	Trypanosoma brucei brucei TREU927	Mutation(s): 0  Gene Names: Tb927.7.1780 EC: 2.4.2.7
UniProt
Find proteins for Q57V32 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1)) Explore Q57V32  Go to UniProtKB:  Q57V32

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HSX	D [auth A], H [auth B]	5-O-phosphono-alpha-D-ribofuranose C5 H11 O8 P KTVPXOYAKDPRHY-AIHAYLRMSA-N
PPV	E [auth A], I [auth B]	PYROPHOSPHATE H4 O7 P2 XPPKVPWEQAFLFU-UHFFFAOYSA-N
ADE	C [auth A], G [auth B]	ADENINE C5 H5 N5 GFFGJBXGBJISGV-UHFFFAOYSA-N
MG	F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free:  0.175 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.143 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.144 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M35VN4

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.84	α = 90
b = 72.85	β = 90
c = 85.61	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
Coot	model building
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-05-24 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2017-05-24
  Type: Initial release
  
• Version 1.1: 2017-06-28
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations
• Version 2.1: 2023-10-04
  Changes: Data collection, Database references, Refinement description, Structure summary