4CKX | pdb_00004ckx

Structure of the Mycobacterium tuberculosis Type II Dehydroquinase N12S mutant (Crystal Form 2)

PDB DOI: https://doi.org/10.2210/pdb4CKX/pdb

Classification: LYASE
Organism(s): Mycobacterium tuberculosis
Expression System: Escherichia coli K-12
Mutation(s): Yes

Deposited: 2014-01-10 Released: 2015-03-25
Deposition Author(s): Otero, J.M., Llamas-Saiz, A.L., Maneiro, M., Peon, A., Sedes, A., Lamb, H., Hawkins, A.R., Gonzalez-Bello, C., van Raaij, M.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.198 (Depositor), 0.193 (DCC)
R-Value Work:
0.143 (Depositor), 0.150 (DCC)
R-Value Observed:
0.145 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 4CKX

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

Literature

Investigation of the Dehydratation Mechanism Catalyzed by the Type II Dehydroquinase

Maneiro, M., Otero, J.M., Peon, A., Sedes, A., Llamas-Saiz, A.L., Lamb, H., Hawkins, A.R., van Raaij, M.J., Gonzalez-Bello, C.

To be published.

Macromolecule Content

Total Structure Weight: 15.77 kDa
Atom Count: 1,073
Modeled Residue Count: 135
Deposited Residue Count: 146
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-DEHYDROQUINATE DEHYDRATASE	A	146	Mycobacterium tuberculosis	Mutation(s): 1 EC: 4.2.1.10
UniProt
Find proteins for P9WPX7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WPX7 Go to UniProtKB: P9WPX7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WPX7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TRS Query on TRS 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]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.198 (Depositor), 0.193 (DCC)
R-Value Work: 0.143 (Depositor), 0.150 (DCC)
R-Value Observed: 0.145 (Depositor)

Space Group: F 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.61	α = 90
b = 125.61	β = 90
c = 125.61	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALE	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2015-03-25

Deposition Author(s):

Llamas-Saiz, A.L.

Gonzalez-Bello, C.

van Raaij, M.J.

Revision History (Full details and data files)

Version 1.0: 2015-03-25
Type: Initial release
Version 1.1: 2018-01-24
Changes: Database references
Version 1.2: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.