5DM5 | pdb_00005dm5

Crystal structure of the hexameric thioesterase y2039 from Yersinia pestis

PDB DOI: https://doi.org/10.2210/pdb5DM5/pdb

Classification: HYDROLASE
Organism(s): Yersinia pestis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-09-08 Released: 2015-11-11
Deposition Author(s): Swarbrick, C.M.D., Forwood, J.K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.262 (Depositor), 0.260 (DCC)
R-Value Work:
0.227 (Depositor), 0.227 (DCC)
R-Value Observed:
0.230 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of the hexameric thioesterase y2039 from Yersinia pestis

Swarbrick, C.M.D., Forwood, J.K.

To be published.

Macromolecule Content

Total Structure Weight: 97.52 kDa
Atom Count: 5,475
Modeled Residue Count: 725
Deposited Residue Count: 912
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative acyl-CoA thioester hydrolase	A, B, C, D, E A, B, C, D, E, F	152	Yersinia pestis	Mutation(s): 0 Gene Names: y2039, YPO2195 EC: 3.1.2
UniProt
Find proteins for A0A5P8YGN6 (Yersinia pestis) Explore A0A5P8YGN6 Go to UniProtKB: A0A5P8YGN6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A5P8YGN6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain I [auth C] SDF format, chain J [auth D] MOL2 format, chain H [auth B] MOL2 format, chain I [auth C] MOL2 format, chain J [auth D] mmCIF format, chain H [auth B] mmCIF format, chain I [auth C] mmCIF format, chain J [auth D]	H [auth B], I [auth C], J [auth D]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth D] Interactions & Density Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain K [auth E] SDF format, chain G [auth A] MOL2 format, chain K [auth E] MOL2 format, chain G [auth A] mmCIF format, chain K [auth E] mmCIF format, chain G [auth A]	G [auth A], K [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain K [auth E] Interactions & Density Focus chain G [auth A] Focus chain K [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.262 (Depositor), 0.260 (DCC)
R-Value Work: 0.227 (Depositor), 0.227 (DCC)
R-Value Observed: 0.230 (Depositor)

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.87	α = 90
b = 77.87	β = 90
c = 285.26	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PHASER	phasing
MOSFLM	data reduction

Structure Validation

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Entry History

Deposition Data

Released Date: 2015-11-11

Deposition Author(s):

Swarbrick, C.M.D.

Forwood, J.K.

Revision History (Full details and data files)

Version 1.0: 2015-11-11
Type: Initial release
Version 1.1: 2017-08-23
Changes: Data collection, Derived calculations
Version 1.2: 2023-09-27
Changes: Data collection, Database references, Refinement description

5DM5 | pdb_00005dm5

Crystal structure of the hexameric thioesterase y2039 from Yersinia pestis

Literature

Crystal structure of the hexameric thioesterase y2039 from Yersinia pestis

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Entry History

Deposition Data

Revision History (Full details and data files)