5T06 | pdb_00005t06

Crystal structure of a putative acyl-CoA thioesterase EC709/ECK0725 from Escherichia coli in complex with Hexanoyl-CoA

PDB DOI: https://doi.org/10.2210/pdb5T06/pdb

Classification: HYDROLASE
Organism(s): Escherichia coli O157:H7
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2016-08-15 Released: 2016-09-07
Deposition Author(s): Watanabe, N., Stogios, P.J., Skarina, T., Di Leo, R., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.213 (Depositor), 0.210 (DCC)
R-Value Work:
0.172 (Depositor), 0.170 (DCC)
R-Value Observed:
0.174 (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 of a putative acyl-CoA thioesterase EC709/ECK0725 from Escherichia coli in complex with Hexanoyl-CoA

Watanabe, N., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 63.26 kDa
Atom Count: 4,791
Modeled Residue Count: 515
Deposited Residue Count: 536
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acyl-CoA thioester hydrolase YbgC	A, B, C, D	134	Escherichia coli O157:H7	Mutation(s): 1 Gene Names: ybgC, Z0904, ECs0771 EC: 3.1.2
UniProt
Find proteins for P0A8Z3 (Escherichia coli (strain K12)) Explore P0A8Z3 Go to UniProtKB: P0A8Z3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A8Z3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HXC Query on HXC Download Ideal Coordinates CCD File SDF format, chain H [auth C] MOL2 format, chain H [auth C] mmCIF format, chain H [auth C]	H [auth C]	HEXANOYL-COENZYME A C₂₇ H₄₆ N₇ O₁₇ P₃ S OEXFMSFODMQEPE-HDRQGHTBSA-N		Interactions Focus chain H [auth C] Interactions & Density Focus chain H [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain J [auth C] SDF format, chain K [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain J [auth C] MOL2 format, chain K [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain J [auth C] mmCIF format, chain K [auth D]	E [auth A] F [auth B] G [auth B] I [auth C] J [auth C] E [auth A], F [auth B], G [auth B], I [auth C], J [auth C], K [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.213 (Depositor), 0.210 (DCC)
R-Value Work: 0.172 (Depositor), 0.170 (DCC)
R-Value Observed: 0.174 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.747	α = 90
b = 96.772	β = 90
c = 97.61	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
Coot	model building

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-09-07

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2016-09-07
Type: Initial release
Version 1.1: 2016-12-28
Changes: Database references
Version 1.2: 2023-10-04
Changes: Data collection, Database references, Refinement description, Structure summary

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Deposit Data

Help and Resources

.id_divider{ color: #ccc; padding: 0 10px 0 10px; } .extended_id_info{ color: #ccc; font-size: 18px; position: relative; top: -10px; left: 4px; } 5T06 | pdb_00005t06

Crystal structure of a putative acyl-CoA thioesterase EC709/ECK0725 from Escherichia coli in complex with Hexanoyl-CoA

Crystal structure of a putative acyl-CoA thioesterase EC709/ECK0725 from Escherichia coli in complex with Hexanoyl-CoA

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)

5T06 | pdb_00005t06