3LM8

Crystal Structure of Thiamine pyrophosphokinase from Bacillus subtilis, Northeast Structural Genomics Consortium Target SR677

PDB DOI: https://doi.org/10.2210/pdb3LM8/pdb

Classification: TRANSFERASE
Organism(s): Bacillus subtilis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2010-01-29 Released: 2010-03-23
Deposition Author(s): Kuzin, A., Abashidze, M., Seetharaman, J., Mao, M., Xiao, R., Foote, E.L., Ciccosanti, C., Wang, H., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.253
R-Value Work: 0.213
R-Value Observed: 0.213

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Northeast Structural Genomics Consortium Target SR677

Kuzin, A., Abashidze, M., Seetharaman, J., Mao, M., Xiao, R., Foote, E.L., Ciccosanti, C., Wang, H., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L.

To be published.

Macromolecule Content

Total Structure Weight: 103.03 kDa
Atom Count: 6,941
Modelled Residue Count: 853
Deposited Residue Count: 888
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thiamine pyrophosphokinase	A, B, C, D	222	Bacillus subtilis	Mutation(s): 1 Gene Names: BSU15800, thiN, yloS EC: 2.7.6.2
UniProt
Find proteins for O34664 (Bacillus subtilis (strain 168)) Explore O34664 Go to UniProtKB: O34664
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O34664
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
VIB Query on VIB Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain O [auth C] SDF format, chain Q [auth D] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain O [auth C] MOL2 format, chain Q [auth D]	E [auth A], I [auth B], O [auth C], Q [auth D]	3-(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-5-(2-HYDROXY-ETHYL)-4-METHYL-THIAZOL-3-IUM C₁₂ H₁₇ N₄ O S JZRWCGZRTZMZEH-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain O [auth C] Focus chain Q [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain O [auth C] Focus chain Q [auth D]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain P [auth C] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain P [auth C]	F [auth A], J [auth B], K [auth B], P [auth C]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain P [auth C] Interactions & Density Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain P [auth C]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B]	G [auth A], H [auth A], L [auth B], M [auth B], N [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B]

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: 2.60 Å
R-Value Free: 0.253
R-Value Work: 0.213
R-Value Observed: 0.213
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.943	α = 82.89
b = 62.153	β = 82.02
c = 84.161	γ = 87.61

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
BALBES	phasing
REFMAC	refinement

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-03-23

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2010-03-23
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2019-07-17
Changes: Data collection, Derived calculations, Refinement description
Version 1.3: 2021-10-13
Changes: Database references, Derived calculations, Structure summary
Version 1.4: 2023-09-06
Changes: Data collection, Refinement description
Version 1.5: 2023-11-22
Changes: Data collection

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Help and Resources

3LM8

Crystal Structure of Thiamine pyrophosphokinase from Bacillus subtilis, Northeast Structural Genomics Consortium Target SR677

Northeast Structural Genomics Consortium Target SR677

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)