3HEM

Structure of Mycobacterium tuberculosis Mycolic Acid Cyclopropane Synthase CmaA2 in Complex with Dioctylamine

PDB DOI: https://doi.org/10.2210/pdb3HEM/pdb

Classification: TRANSFERASE
Organism(s): Mycobacterium tuberculosis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-05-09 Released: 2009-06-16
Deposition Author(s): Liu, Z., Sacchettini, J.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.39 Å
R-Value Free: 0.266
R-Value Work: 0.243

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Structure of Mycobacterium tuberculosis Mycolic Acid Cyclopropane Synthase CmaA2 in Complex with Dioctylamine

Barkan, D., Liu, Z., Sacchettini, J.C., Glickman, M.S.

To be published.

Macromolecule Content

Total Structure Weight: 34.94 kDa
Atom Count: 2,402
Modelled Residue Count: 291
Deposited Residue Count: 302
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclopropane-fatty-acyl-phospholipid synthase 2	A	302	Mycobacterium tuberculosis	Mutation(s): 0 Gene Names: cma2, cmaA2, MT0524, MTCY20G9.30c, Rv0503c EC: 2.1.1.79
UniProt
Find proteins for P9WPB5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WPB5 Go to UniProtKB: P9WPB5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WPB5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
D22 Query on D22 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	N-octyloctan-1-amine C₁₆ H₃₅ N LAWOZCWGWDVVSG-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
CO3 Query on CO3 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	CARBONATE ION C O₃ BVKZGUZCCUSVTD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.39 Å
R-Value Free: 0.266
R-Value Work: 0.243
Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.857	α = 90
b = 106.857	β = 90
c = 224.979	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
DENZO	data reduction
SCALEPACK	data scaling
PROCESS	data scaling
XFIT	data reduction

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-06-16

Deposition Author(s):

Liu, Z.

Sacchettini, J.C.

Revision History (Full details and data files)

Version 1.0: 2009-06-16
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2024-02-21
Changes: Data collection, Database references, Derived calculations

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3HEM

Structure of Mycobacterium tuberculosis Mycolic Acid Cyclopropane Synthase CmaA2 in Complex with Dioctylamine

Structure of Mycobacterium tuberculosis Mycolic Acid Cyclopropane Synthase CmaA2 in Complex with Dioctylamine

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)