5JJU | pdb_00005jju

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.31 Å
R-Value Free:
0.288 (Depositor), 0.281 (DCC)
R-Value Work:
0.217 (Depositor), 0.220 (DCC)
R-Value Observed:
0.221 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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 Biological Chem 291: 14386-14387

PubMed: 27371563 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1074/jbc.A115.699801
Primary Citation Related Structures:
5JJU

Macromolecule Content

Total Structure Weight: 73.04 kDa
Atom Count: 5,061
Modeled Residue Count: 652
Deposited Residue Count: 682
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein Rv2837c	A, B	340	Mycobacterium tuberculosis H37Ra	Mutation(s): 0 EC: 3.1 (UniProt), 3.1.3.7 (UniProt)
UniProt
Find proteins for P71615 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P71615 Go to UniProtKB: P71615
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P71615
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism
Entity ID: 2
RNA (5'-R(PAPA)-3')	C	2	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AMP Query on AMP Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B]	H [auth B], I [auth B]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain H [auth B] Focus chain I [auth B]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain F [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], F [auth B], G [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.31 Å
R-Value Free: 0.288 (Depositor), 0.281 (DCC)
R-Value Work: 0.217 (Depositor), 0.220 (DCC)
R-Value Observed: 0.221 (Depositor)

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

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2016-05-04

Deposition Author(s):

This entry supersedes: 5CEU

Revision History (Full details and data files)

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

5JJU | pdb_00005jju

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

Literature

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

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Entity ID: 2