3K94 | pdb_00003k94

Crystal Structure of Thiamin pyrophosphokinase from Geobacillus thermodenitrificans, Northeast Structural Genomics Consortium Target GtR2

PDB DOI: https://doi.org/10.2210/pdb3K94/pdb

Classification: TRANSFERASE
Organism(s): Geobacillus thermodenitrificans NG80-2
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2009-10-15 Released: 2010-02-09
Deposition Author(s): Kuzin, A., Su, M., Seetharaman, J., Janjua, J., Xiao, R., Patel, D.J., Ciccosanti, C., Lee, D., 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: 2.10 Å
R-Value Free:
0.242 (Depositor), 0.233 (DCC)
R-Value Work:
0.177 (Depositor), 0.171 (DCC)
R-Value Observed:
0.180 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Northeast Structural Genomics Consortium Target GtR2

Kuzin, A., Su, M., Seetharaman, J., Janjua, J., Xiao, R., Patel, D.J., Ciccosanti, C., Lee, D., 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: 50.97 kDa
Atom Count: 3,642
Modeled Residue Count: 431
Deposited Residue Count: 446
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thiamin pyrophosphokinase	A, B	223	Geobacillus thermodenitrificans NG80-2	Mutation(s): 0 Gene Names: GTNG_1032 EC: 2.7.6.2
UniProt
Find proteins for A4IM54 (Geobacillus thermodenitrificans (strain NG80-2)) Explore A4IM54 Go to UniProtKB: A4IM54
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A4IM54
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO Query on CSO	A, B	L-PEPTIDE LINKING	C₃ H₇ N O₃ S		CYS
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.242 (Depositor), 0.233 (DCC)
R-Value Work: 0.177 (Depositor), 0.171 (DCC)
R-Value Observed: 0.180 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.422	α = 90
b = 73.652	β = 90
c = 82.657	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
PHENIX	phasing
REFMAC	refinement

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-02-09

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2010-02-09
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.2: 2019-07-17
Changes: Data collection, Derived calculations, Refinement description
Version 1.3: 2024-11-06
Changes: Data collection, Database references, Structure summary