9JV8 | pdb_00009jv8

Crystal structure of M. tuberculosis EccCb1-D2 domain

PDB DOI: https://doi.org/10.2210/pdb9JV8/pdb

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

Deposited: 2024-10-08 Released: 2025-10-08
Deposition Author(s): Saxena, A.K.
Funding Organization(s): Science and Engineering Research Board (SERB)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.229 (Depositor), 0.229 (DCC)
R-Value Work:
0.177 (Depositor), 0.181 (DCC)
R-Value Observed:
0.182 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

M. tuberculosis EccCb1-D2 domain

Saxena, A.K.

To be published.

Macromolecule Content

Total Structure Weight: 34.95 kDa
Atom Count: 2,346
Modeled Residue Count: 280
Deposited Residue Count: 312
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ESX-1 secretion system protein EccCb1	A	312	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: eccCb1, snm2, Rv3871
UniProt
Find proteins for P9WNB1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WNB1 Go to UniProtKB: P9WNB1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WNB1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP (Subject of Investigation/LOI) Query on ATP Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.229 (Depositor), 0.229 (DCC)
R-Value Work: 0.177 (Depositor), 0.181 (DCC)
R-Value Observed: 0.182 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.389	α = 90
b = 75.642	β = 90
c = 102.524	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
PHASER	phasing
HKL-3000	data reduction

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-10-08

Deposition Author(s):

Funding Organization	Location	Grant Number
Science and Engineering Research Board (SERB)	India	EMR/2016/000867

Revision History (Full details and data files)

Version 1.0: 2025-10-08
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.