4MUU | pdb_00004muu

Structure of ThiT with pyrithiamine bound

• PDB DOI: https://doi.org/10.2210/pdb4MUU/pdb

• Classification: THIAMINE BINDING PROTEIN
• Organism(s): Lactococcus cremoris subsp. cremoris NZ9000
• Expression System: Lactococcus cremoris subsp. cremoris NZ9000
• Mutation(s): No 


• Deposited: 2013-09-23 Released: 2014-09-17 
• Deposition Author(s): Swier, L.J.Y.M., Guskov, A., Slotboom, D.J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.236 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

Structural studies on the thiamin binding protein ThiT

Swier, L.J.Y.M., Gomez, L., Guskov, A., Hirsch, A.K.H., Slotboom, D.J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 49.89 kDa 
• Atom Count: 3,380 
• Modeled Residue Count: 355 
• Deposited Residue Count: 384 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thiamine transporter ThiT	A, B	192	Lactococcus cremoris subsp. cremoris NZ9000	Mutation(s): 0  Gene Names: LLNZ_01755

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PE5	OA [auth B]	3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL C18 H38 O9 CUDPPTPIUWYGFI-UHFFFAOYSA-N
BNG	AA [auth B], D [auth A], Z [auth B]	nonyl beta-D-glucopyranoside C15 H30 O6 QFAPUKLCALRPLH-UXXRCYHCSA-N
P6G	EA [auth B], FA [auth B], GA [auth B], HA [auth B]	HEXAETHYLENE GLYCOL C12 H26 O7 IIRDTKBZINWQAW-UHFFFAOYSA-N
218	C [auth A], Y [auth B]	1-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-(2-HYDROXYETHYL)-2-METHYLPYRIDINIUM C14 H19 N4 O PZWYDZMWPANLMB-UHFFFAOYSA-N
1PE	W [auth A]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
PG4	KA [auth B], LA [auth B], MA [auth B], NA [auth B], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE	PA [auth B], QA [auth B], X [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PG0	IA [auth B], JA [auth B], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A]	2-(2-METHOXYETHOXY)ETHANOL C5 H12 O3 SBASXUCJHJRPEV-UHFFFAOYSA-N
PEG	BA [auth B], CA [auth B], DA [auth B], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.236 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.56	α = 90
b = 84.59	β = 95.61
c = 127.26	γ = 90

Software Package:

Software Name	Purpose
MxCuBE	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-09-17 
Deposition Author(s): Swier, L.J.Y.M., Guskov, A., Slotboom, D.J.

Revision History  

• Version 1.0: 2014-09-17
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Refinement description, Structure summary