6YR3 | pdb_00006yr3

1.48 Angstrom Resolution Crystal Structure of Transaldolase from Thermoplasma acidophilum in complex with D-fructose 6-phosphate Schiff-base intermediate

PDB DOI: https://doi.org/10.2210/pdb6YR3/pdb

Classification: TRANSFERASE
Organism(s): Thermoplasma acidophilum DSM 1728
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-04-19 Released: 2021-04-28
Deposition Author(s): Sautner, V., Tittmann, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.48 Å
R-Value Free:
0.186 (Depositor), 0.190 (DCC)
R-Value Work:
0.160 (Depositor), 0.160 (DCC)
R-Value Observed:
0.161 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Large-scale motions underlie physical but not chemical steps in transaldolase mechanism: Substrate binding by conformational selection and rate-determining product release

Sautner, V., Lietzow, T.H., Klaus, M., Funk, L.M., Tittmann, K.

To be published.

Macromolecule Content

Total Structure Weight: 124.59 kDa
Atom Count: 10,377
Modeled Residue Count: 1,115
Deposited Residue Count: 1,115
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable transaldolase	A, B, C, D, E	223	Thermoplasma acidophilum DSM 1728	Mutation(s): 0 Gene Names: tal, Ta0616 EC: 2.2.1.2
UniProt
Find proteins for Q9HKI3 (Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165)) Explore Q9HKI3 Go to UniProtKB: Q9HKI3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9HKI3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
F6R (Subject of Investigation/LOI) Query on F6R Download Ideal Coordinates CCD File SDF format, chain M [auth C] SDF format, chain P [auth D] SDF format, chain R [auth E] SDF format, chain F [auth A] SDF format, chain J [auth B] MOL2 format, chain M [auth C] MOL2 format, chain P [auth D] MOL2 format, chain R [auth E] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] mmCIF format, chain M [auth C] mmCIF format, chain P [auth D] mmCIF format, chain R [auth E] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B]	F [auth A], J [auth B], M [auth C], P [auth D], R [auth E]	FRUCTOSE -6-PHOSPHATE C₆ H₁₃ O₉ P GSXOAOHZAIYLCY-HSUXUTPPSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D] Focus chain R [auth E] Interactions & Density Focus chain F [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D] Focus chain R [auth E]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain N [auth C] SDF format, chain Q [auth D] SDF format, chain S [auth E] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain S [auth E] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain N [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain S [auth E]	G [auth A], K [auth B], N [auth C], Q [auth D], S [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain Q [auth D] Focus chain S [auth E] Interactions & Density Focus chain G [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain Q [auth D] Focus chain S [auth E]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain O [auth C] SDF format, chain T [auth E] SDF format, chain U [auth E] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain O [auth C] MOL2 format, chain T [auth E] MOL2 format, chain U [auth E] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain O [auth C] mmCIF format, chain T [auth E] mmCIF format, chain U [auth E]	H [auth A] I [auth A] L [auth B] O [auth C] T [auth E] H [auth A], I [auth A], L [auth B], O [auth C], T [auth E], U [auth E]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain T [auth E] Focus chain U [auth E] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain T [auth E] Focus chain U [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.48 Å
R-Value Free: 0.186 (Depositor), 0.190 (DCC)
R-Value Work: 0.160 (Depositor), 0.160 (DCC)
R-Value Observed: 0.161 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 148.51	α = 90
b = 172.2	β = 90
c = 100.58	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2021-04-28

Deposition Author(s):

Sautner, V.

Tittmann, K.

Revision History (Full details and data files)

Version 1.0: 2021-04-28
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-11-20
Changes: Structure summary