1U5V

Structure of CitE complexed with triphosphate group of ATP form Mycobacterium tuberculosis

PDB DOI: https://doi.org/10.2210/pdb1U5V/pdb

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

Deposited: 2004-07-28 Released: 2004-10-12
Deposition Author(s): Goulding, C.W., Lerkin, T., Kim, C.Y., Segelke, B., Terwilliger, T., Eisenberg, E., TB Structural Genomics Consortium (TBSGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.234
R-Value Work: 0.212
R-Value Observed: 0.212

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.6 of the entry. See complete history.

Literature

Crystal structure of Mycobacterium tuberculosis citrate lyase beta subunit and its unusual triphosphate binding site

Goulding, C.W., Lerkin, T., Kim, C.Y., Segelke, B., Terwilliger, T., Eisenberg, E.

To be published.

Macromolecule Content

Total Structure Weight: 29.07 kDa
Atom Count: 1,804
Modelled Residue Count: 223
Deposited Residue Count: 273
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
citE	A	273	Mycobacterium tuberculosis	Mutation(s): 6 Gene Names: Rv2498c EC: 4.1.3.6 (PDB Primary Data), 4.1 (UniProt)
UniProt
Find proteins for P9WPE1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WPE1 Go to UniProtKB: P9WPE1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WPE1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP 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]
FMT Query on FMT 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]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-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: 1.85 Å
R-Value Free: 0.234
R-Value Work: 0.212
R-Value Observed: 0.212
Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.214	α = 90
b = 91.214	β = 90
c = 220.233	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
EPMR	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2004-10-12

Deposition Author(s):

Terwilliger, T.

TB Structural Genomics Consortium (TBSGC)

Revision History (Full details and data files)

Version 1.0: 2004-10-12
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2016-09-21
Changes: Other
Version 1.4: 2018-10-03
Changes: Data collection, Derived calculations
Version 1.5: 2021-10-20
Changes: Database references, Derived calculations
Version 1.6: 2023-08-23
Changes: Data collection, Refinement description

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.