6YRM | pdb_00006yrm

Transaldolase variant T30A from T. acidophilum in complex with D-fructose 6-phosphate Schiff-base intermediate

PDB DOI: https://doi.org/10.2210/pdb6YRM/pdb

Classification: TRANSFERASE
Organism(s): Thermoplasma acidophilum DSM 1728
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2020-04-20 Released: 2021-05-12
Deposition Author(s): Sautner, V., Klaus, M., Tittmann, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.205 (Depositor), 0.205 (DCC)
R-Value Work:
0.174 (Depositor), 0.177 (DCC)
R-Value Observed:
0.176 (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: 124.5 kDa
Atom Count: 9,557
Modeled Residue Count: 1,115
Deposited Residue Count: 1,115
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 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): 2 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 F [auth A] SDF format, chain J [auth B] SDF format, chain M [auth C] SDF format, chain Q [auth D] SDF format, chain S [auth E] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain S [auth E] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain M [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain S [auth E]	F [auth A], J [auth B], M [auth C], Q [auth D], S [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 Q [auth D] Focus chain S [auth E] Interactions & Density Focus chain F [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain Q [auth D] Focus chain S [auth E]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain K [auth B] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain R [auth D] SDF format, chain T [auth E] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain R [auth D] MOL2 format, chain T [auth E] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain K [auth B] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C] mmCIF format, chain R [auth D] mmCIF format, chain T [auth E]	G [auth A] H [auth A] K [auth B] N [auth C] O [auth C] G [auth A], H [auth A], K [auth B], N [auth C], O [auth C], R [auth D], T [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain R [auth D] Focus chain T [auth E] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain R [auth D] Focus chain T [auth E]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain P [auth C] SDF format, chain U [auth E] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain P [auth C] MOL2 format, chain U [auth E] mmCIF format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain P [auth C] mmCIF format, chain U [auth E]	I [auth A], L [auth B], P [auth C], U [auth E]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain U [auth E] Interactions & Density Focus chain I [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain U [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.205 (Depositor), 0.205 (DCC)
R-Value Work: 0.174 (Depositor), 0.177 (DCC)
R-Value Observed: 0.176 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 148.6	α = 90
b = 172.27	β = 90
c = 99.95	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

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2021-05-12

Deposition Author(s):

Sautner, V.

Klaus, M.

Tittmann, K.

Revision History (Full details and data files)

Version 1.0: 2021-05-12
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-11-13
Changes: Structure summary