9M1Q | pdb_00009m1q

Crystal structure of N-terminal domain of hypothetical protein Rv1421 from Mycobacterium tuberculosis H37Rv

PDB DOI: https://doi.org/10.2210/pdb9M1Q/pdb

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

Deposited: 2025-02-26 Released: 2025-04-30
Deposition Author(s): Lee, K.S., Park, J.
Funding Organization(s): National Research Foundation (NRF, Korea)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.265 (Depositor), 0.266 (DCC)
R-Value Work:
0.229 (Depositor), 0.229 (DCC)
R-Value Observed:
0.231 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structural insight of N-terminal domain of hypothetical protein Rv1421 from Mycobacterium tuberculosis H37Rv

Lee, K.S., Park, J.

To be published.

Macromolecule Content

Total Structure Weight: 37.69 kDa
Atom Count: 2,556
Modeled Residue Count: 312
Deposited Residue Count: 348
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleotide-binding protein Rv1421	A, B	174	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: Rv1421, MTCY21B4.39
UniProt
Find proteins for P9WFQ3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WFQ3 Go to UniProtKB: P9WFQ3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WFQ3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P6G (Subject of Investigation/LOI) Query on P6G 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]	HEXAETHYLENE GLYCOL C₁₂ H₂₆ O₇ IIRDTKBZINWQAW-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: 1.70 Å
R-Value Free: 0.265 (Depositor), 0.266 (DCC)
R-Value Work: 0.229 (Depositor), 0.229 (DCC)
R-Value Observed: 0.231 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.008	α = 90
b = 58.547	β = 133.116
c = 84.87	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-04-30

Deposition Author(s):

Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	2021R1F1A1047349

Revision History (Full details and data files)

Version 1.0: 2025-04-30
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.