4YZO

Crystal Structure Analysis of Thiolase-like protein, ST0096 from Sulfolobus Tokodaii

PDB DOI: https://doi.org/10.2210/pdb4YZO/pdb

Classification: TRANSFERASE
Organism(s): Sulfurisphaera tokodaii str. 7
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-03-25 Released: 2016-03-30
Deposition Author(s): Padmanabhan, B., Manjula, R., Yokoyama, S., Bessho, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.194
R-Value Work: 0.162
R-Value Observed: 0.164

wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure Analysis of Thiolase-like protein, ST0096 from Sulfolobus Tokodaii

Padmanabhan, B., Manjula, R., Yokoyama, S., Bessho, Y.

To be published.

Macromolecule Content

Total Structure Weight: 164.71 kDa
Atom Count: 12,627
Modelled Residue Count: 1,411
Deposited Residue Count: 1,492
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative acyl-CoA acyltransferase	A, B, C, D	373	Sulfurisphaera tokodaii str. 7	Mutation(s): 0 Gene Names: STK_00960 EC: 2.3.1
UniProt
Find proteins for Q976U3 (Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)) Explore Q976U3 Go to UniProtKB: Q976U3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q976U3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain K [auth C] SDF format, chain L [auth C] SDF format, chain M [auth C] SDF format, chain O [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C] MOL2 format, chain O [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain K [auth C] mmCIF format, chain L [auth C] mmCIF format, chain M [auth C] mmCIF format, chain O [auth D]	E [auth A] F [auth A] H [auth B] I [auth B] K [auth C] E [auth A], F [auth A], H [auth B], I [auth B], K [auth C], L [auth C], M [auth C], O [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Focus chain O [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Focus chain O [auth D]
IMD Query on IMD Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B] mmCIF format, chain J [auth B]	J [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain N [auth C] SDF format, chain P [auth D] MOL2 format, chain N [auth C] MOL2 format, chain P [auth D] mmCIF format, chain N [auth C] mmCIF format, chain P [auth D]	N [auth C], P [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain N [auth C] Focus chain P [auth D] Interactions & Density Focus chain N [auth C] Focus chain P [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.194
R-Value Work: 0.162
R-Value Observed: 0.164
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 152.763	α = 90
b = 80.863	β = 110.8
c = 137.512	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2016-03-30

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-03-30
Type: Initial release
Version 1.1: 2020-02-19
Changes: Data collection, Derived calculations
Version 1.2: 2024-10-09
Changes: Data collection, Database references, Derived calculations, Structure summary