1YLI | pdb_00001yli

Crystal structure of HI0827, a hexameric broad specificity acyl-coenzyme A thioesterase

PDB DOI: https://doi.org/10.2210/pdb1YLI/pdb
Entry: 1YLI supersedes: 1NNG

Classification: HYDROLASE
Organism(s): Haemophilus influenzae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2005-01-19 Released: 2005-02-01
Deposition Author(s): Structure 2 Function Project (S2F)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.227 (Depositor), 0.230 (DCC)
R-Value Work:
0.180 (Depositor), 0.185 (DCC)
R-Value Observed:
0.184 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

STRUCTURE OF HI0827, A THIOESTERASE ACTING ON SHORT-CHAIN ACYL-COA COMPOUNDS

Willis, M.A., Zhuang, Z., Song, F., Howard, A., Dunaway-Mariano, D., Herzberg, O.

To be published.

Macromolecule Content

Total Structure Weight: 35.18 kDa
Atom Count: 2,537
Modeled Residue Count: 290
Deposited Residue Count: 306
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative acyl-CoA thioester hydrolase HI0827	A, B	153	Haemophilus influenzae	Mutation(s): 0 Gene Names: YCIA-HAEIN EC: 3.1.2
UniProt
Find proteins for P44886 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)) Explore P44886 Go to UniProtKB: P44886
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P44886
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
COA Query on COA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B]	E [auth A], H [auth B]	COENZYME A C₂₁ H₃₆ N₇ O₁₆ P₃ S RGJOEKWQDUBAIZ-IBOSZNHHSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B]	I [auth B], J [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain I [auth B] Focus chain J [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain F [auth B] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B]	C [auth A], D [auth A], F [auth B], G [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth B] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth B] Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.227 (Depositor), 0.230 (DCC)
R-Value Work: 0.180 (Depositor), 0.185 (DCC)
R-Value Observed: 0.184 (Depositor)

Space Group: I 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 163.676	α = 90
b = 163.676	β = 90
c = 163.676	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2005-02-01

Deposition Author(s):

Structure 2 Function Project (S2F)

This entry supersedes: 1NNG

Revision History (Full details and data files)

Version 1.0: 2005-02-01
Type: Initial release
Version 1.1: 2007-12-17
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Derived calculations, Version format compliance
Version 1.3: 2017-10-11
Changes: Refinement description
Version 1.4: 2024-02-14
Changes: Data collection, Database references, Derived calculations

1YLI | pdb_00001yli

Crystal structure of HI0827, a hexameric broad specificity acyl-coenzyme A thioesterase

Literature

STRUCTURE OF HI0827, A THIOESTERASE ACTING ON SHORT-CHAIN ACYL-COA COMPOUNDS

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand