5JJU

Crystal structure of Rv2837c complexed with 5'-pApA and 5'-AMP

• PDB DOI: https://doi.org/10.2210/pdb5JJU/pdb
• Entry: 5JJU supersedes: 5CEU
• NAKB: 5JJU

• Classification: HYDROLASE/RNA
• Organism(s): Mycobacterium tuberculosis H37Ra, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-04-25 Released: 2016-05-04 
• Deposition Author(s): Wang, F., He, Q., Liu, S., Gu, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.31 Å
• R-Value Free: 0.288 
• R-Value Work: 0.217 
• R-Value Observed: 0.221 

Literature

Structural and biochemical insight into the mechanism of Rv2837c from Mycobacterium tuberculosis as a c-di-NMP phosphodiesterase

He, Q., Wang, F., Liu, S., Zhu, D., Cong, H., Gao, F., Li, B., Wang, H., Lin, Z., Liao, J., Gu, L.

(2016) J Biol Chem 291: 14386-14387

• PubMed: 27371563 
• DOI: https://doi.org/10.1074/jbc.A115.699801
• Primary Citation of Related Structures:  
  5JJU

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: 73.04 kDa 
• Atom Count: 5,061 
• Modelled Residue Count: 652 
• Deposited Residue Count: 682 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein Rv2837c	A, B	340	Mycobacterium tuberculosis H37Ra	Mutation(s): 0
UniProt
Find proteins for A5U6I9 (Mycobacterium tuberculosis (strain ATCC 25177 / H37Ra)) Explore A5U6I9  Go to UniProtKB:  A5U6I9

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*AP*A)-3')	C	2	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP	H [auth B], I [auth B]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
MN	D [auth A], E [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: 2.31 Å
• R-Value Free: 0.288 
• R-Value Work: 0.217 
• R-Value Observed: 0.221 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.374	α = 90
b = 99.267	β = 90
c = 108.677	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-05-04 
Deposition Author(s): Wang, F., He, Q., Liu, S., Gu, L.
• This entry supersedes: 5CEU

Revision History  

• Version 1.0: 2016-05-04
  Type: Initial release
  
• Version 1.1: 2016-10-12
  Changes: Database references, Other
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references, Derived calculations