5C7S | pdb_00005c7s

PRPP complexed with two Mn2+ in the active site of Mycobacterium tuberculosis anthranilate phosphoribosyltransferase (AnPRT; trpD)

• PDB DOI: https://doi.org/10.2210/pdb5C7S/pdb

• Classification: TRANSFERASE
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-06-24 Released: 2016-06-29 
• Deposition Author(s): Evans, G.L., Baker, E.N., Lott, J.S., TB Structural Genomics Consortium (TBSGC)
• Funding Organization(s): Health Research Council (HRC), FRST (Foundation for Research, Science and Technology)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.254 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Starting Model: experimental

Literature

Binding and mimicking of the phosphate-rich substrate, PRPP

Evans, G.L., Baker, E.N., Lott, J.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: 78.9 kDa 
• Atom Count: 5,356 
• Modeled Residue Count: 687 
• Deposited Residue Count: 758 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Anthranilate phosphoribosyltransferase	A, B	379	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: trpD, Rv2192c, MTCY190.03c EC: 2.4.2.18
UniProt
Find proteins for P9WFX5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WFX5  Go to UniProtKB:  P9WFX5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PRP	E [auth A], H [auth B]	1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose C5 H13 O14 P3 PQGCEDQWHSBAJP-TXICZTDVSA-N
MN	C [auth A], D [auth A], F [auth B], G [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.254 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.178	α = 90
b = 78.481	β = 109.9
c = 100.446	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data scaling
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
Blu-Ice	data collection
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-06-29 
Deposition Author(s): Evans, G.L., Baker, E.N., Lott, J.S., TB Structural Genomics Consortium (TBSGC)

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Funding Organization	Location	Grant Number
Health Research Council (HRC)	New Zealand	HRC12/1111
FRST (Foundation for Research, Science and Technology)	New Zealand	UOAX1005

Revision History  

• Version 1.0: 2016-06-29
  Type: Initial release
  
• Version 1.1: 2017-09-13
  Changes: Author supporting evidence, Derived calculations
• Version 1.2: 2017-11-22
  Changes: Refinement description
• Version 1.3: 2019-07-17
  Changes: Data collection, Refinement description
• Version 1.4: 2020-01-01
  Changes: Author supporting evidence
• Version 1.5: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.6: 2023-09-27
  Changes: Data collection, Database references, Refinement description, Structure summary