4FND | pdb_00004fnd

Crystal structure of the Mtb enoyl CoA isomerase in complex with hydroxyhexanoyl CoA

PDB DOI: https://doi.org/10.2210/pdb4FND/pdb

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

Deposited: 2012-06-19 Released: 2013-05-29
Deposition Author(s): Bruning, J.B., Gao, N., Hernandez, E.D., Li, H., Dang, N., Hung, L.W., Sacchettini, J.C., TB Structural Genomics Consortium (TBSGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.240 (Depositor), 0.227 (DCC)
R-Value Work:
0.196 (Depositor), 0.186 (DCC)
R-Value Observed:
0.198 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure and mechanism of the prokaryotic enoyl CoA isomerase

Bruning, J.B., Gao, N., Hernandez, E.D., Li, H., Dang, N., Hung, L.W., Moran, S., Sacchettini, J.C.

To be published.

Macromolecule Content

Total Structure Weight: 25.54 kDa
Atom Count: 2,089
Modeled Residue Count: 232
Deposited Residue Count: 232
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Enoyl-CoA hydratase/isomerase family protein	A	232	Mycobacterium tuberculosis	Mutation(s): 0 Gene Names: echA3, MT0660, Rv0632c EC: 4.2.1.17
UniProt
Find proteins for I6Y8B5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore I6Y8B5 Go to UniProtKB: I6Y8B5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	I6Y8B5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3H9 Query on 3H9 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]	(S)-3-Hydroxyhexanoyl-CoA C₂₇ H₄₂ N₇ O₁₈ P₃ S VAAHKRMGOFIORX-IKTBLOROSA-J		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	C [auth A], D [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.240 (Depositor), 0.227 (DCC)
R-Value Work: 0.196 (Depositor), 0.186 (DCC)
R-Value Observed: 0.198 (Depositor)

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.018	α = 90
b = 77.018	β = 90
c = 135.595	γ = 120

Software Package:

Software Name	Purpose
d*TREK	data scaling
d*TREK	data reduction
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-05-29

Deposition Author(s):

TB Structural Genomics Consortium (TBSGC)

Revision History (Full details and data files)

Version 1.0: 2013-05-29
Type: Initial release
Version 1.1: 2018-01-24
Changes: Structure summary
Version 1.2: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description

4FND | pdb_00004fnd

Crystal structure of the Mtb enoyl CoA isomerase in complex with hydroxyhexanoyl CoA

Literature

Crystal structure and mechanism of the prokaryotic enoyl CoA isomerase

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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