3M49 | pdb_00003m49

Crystal Structure of Transketolase Complexed with Thiamine Diphosphate from Bacillus anthracis

PDB DOI: https://doi.org/10.2210/pdb3M49/pdb
Entry: 3M49 supersedes: 3K95

Classification: TRANSFERASE
Organism(s): Bacillus anthracis str. 'Ames Ancestor
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-03-10 Released: 2010-04-07
Deposition Author(s): Maltseva, N., Kim, Y., Kwon, K., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.172 (Depositor), 0.170 (DCC)
R-Value Work:
0.137 (Depositor), 0.134 (DCC)
R-Value Observed:
0.139 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Crystal Structure of Transketolase Complexed with Thiamine Diphosphate from Bacillus anthracis

Maltseva, N., Kim, Y., Kwon, K., Anderson, W.F., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 156.42 kDa
Atom Count: 11,757
Modeled Residue Count: 1,329
Deposited Residue Count: 1,380
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transketolase	A, B	690	Bacillus anthracis str. 'Ames Ancestor	Mutation(s): 0 Gene Names: BAS3470, BA_3744, GBAA3744, GBAA_3744, tkt-2, tkt2 EC: 2.2.1.1
UniProt
Find proteins for A0A6L7H165 (Bacillus anthracis) Explore A0A6L7H165 Go to UniProtKB: A0A6L7H165
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A6L7H165
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 10 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TPP Query on TPP Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain C [auth A] MOL2 format, chain AA [auth B] MOL2 format, chain C [auth A] mmCIF format, chain AA [auth B] mmCIF format, chain C [auth A]	AA [auth B], C [auth A]	THIAMINE DIPHOSPHATE C₁₂ H₁₉ N₄ O₇ P₂ S AYEKOFBPNLCAJY-UHFFFAOYSA-O		Interactions Focus chain AA [auth B] Focus chain C [auth A] Interactions & Density Focus chain AA [auth B] Focus chain C [auth A]
BTB Query on BTB Download:Ideal Coordinates CCD File SDF format, chain CA [auth B] MOL2 format, chain CA [auth B] mmCIF format, chain CA [auth B]	CA [auth B]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₈ H₁₉ N O₅ OWMVSZAMULFTJU-UHFFFAOYSA-N		Interactions Focus chain CA [auth B] Interactions & Density Focus chain CA [auth B]
PG5 Query on PG5 Download:Ideal Coordinates CCD File SDF format, chain N [auth A] MOL2 format, chain N [auth A] mmCIF format, chain N [auth A]	N [auth A]	1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE C₈ H₁₈ O₄ YFNKIDBQEZZDLK-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Interactions & Density Focus chain N [auth A]
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain P [auth A] MOL2 format, chain P [auth A] mmCIF format, chain P [auth A]	P [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain P [auth A] Interactions & Density Focus chain P [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain S [auth A] MOL2 format, chain O [auth A] MOL2 format, chain S [auth A] mmCIF format, chain O [auth A] mmCIF format, chain S [auth A]	O [auth A], S [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain O [auth A] Focus chain S [auth A] Interactions & Density Focus chain O [auth A] Focus chain S [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain D [auth A] SDF format, chain H [auth A] SDF format, chain HA [auth B] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain NA [auth B] SDF format, chain X [auth A] MOL2 format, chain BA [auth B] MOL2 format, chain D [auth A] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth B] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain NA [auth B] MOL2 format, chain X [auth A] mmCIF format, chain BA [auth B] mmCIF format, chain D [auth A] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth B] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain NA [auth B] mmCIF format, chain X [auth A]	BA [auth B] D [auth A] H [auth A] HA [auth B] I [auth A] BA [auth B], D [auth A], H [auth A], HA [auth B], I [auth A], J [auth A], K [auth A], NA [auth B], X [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain BA [auth B] Focus chain D [auth A] Focus chain H [auth A] Focus chain HA [auth B] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain NA [auth B] Focus chain X [auth A] Interactions & Density Focus chain BA [auth B] Focus chain D [auth A] Focus chain H [auth A] Focus chain HA [auth B] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain NA [auth B] Focus chain X [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain EA [auth B] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain JA [auth B] SDF format, chain LA [auth B] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain Z [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain JA [auth B] MOL2 format, chain LA [auth B] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain Z [auth A] mmCIF format, chain EA [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain JA [auth B] mmCIF format, chain LA [auth B] mmCIF format, chain U [auth A] mmCIF format, chain V [auth A] mmCIF format, chain Z [auth A]	EA [auth B] F [auth A] G [auth A] JA [auth B] LA [auth B] EA [auth B], F [auth A], G [auth A], JA [auth B], LA [auth B], U [auth A], V [auth A], Z [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain EA [auth B] Focus chain F [auth A] Focus chain G [auth A] Focus chain JA [auth B] Focus chain LA [auth B] Focus chain U [auth A] Focus chain V [auth A] Focus chain Z [auth A] Interactions & Density Focus chain EA [auth B] Focus chain F [auth A] Focus chain G [auth A] Focus chain JA [auth B] Focus chain LA [auth B] Focus chain U [auth A] Focus chain V [auth A] Focus chain Z [auth A]
ACY Query on ACY Download:Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A] mmCIF format, chain M [auth A]	M [auth A]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain DA [auth B] SDF format, chain E [auth A] SDF format, chain FA [auth B] SDF format, chain GA [auth B] SDF format, chain IA [auth B] SDF format, chain KA [auth B] SDF format, chain L [auth A] SDF format, chain MA [auth B] SDF format, chain Q [auth A] SDF format, chain T [auth A] SDF format, chain Y [auth A] SDF format, chain W [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain E [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain IA [auth B] MOL2 format, chain KA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain MA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain T [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain W [auth A] mmCIF format, chain DA [auth B] mmCIF format, chain E [auth A] mmCIF format, chain FA [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain IA [auth B] mmCIF format, chain KA [auth B] mmCIF format, chain L [auth A] mmCIF format, chain MA [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain T [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain W [auth A]	DA [auth B] E [auth A] FA [auth B] GA [auth B] IA [auth B] DA [auth B], E [auth A], FA [auth B], GA [auth B], IA [auth B], KA [auth B], L [auth A], MA [auth B], Q [auth A], T [auth A], W [auth A], Y [auth A]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain DA [auth B] Focus chain E [auth A] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain IA [auth B] Focus chain KA [auth B] Focus chain L [auth A] Focus chain MA [auth B] Focus chain Q [auth A] Focus chain T [auth A] Focus chain W [auth A] Focus chain Y [auth A] Interactions & Density Focus chain DA [auth B] Focus chain E [auth A] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain IA [auth B] Focus chain KA [auth B] Focus chain L [auth A] Focus chain MA [auth B] Focus chain Q [auth A] Focus chain T [auth A] Focus chain W [auth A] Focus chain Y [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain R [auth A] MOL2 format, chain R [auth A] mmCIF format, chain R [auth A]	R [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain R [auth A] Interactions & Density Focus chain R [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
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: 2.00 Å
R-Value Free: 0.172 (Depositor), 0.170 (DCC)
R-Value Work: 0.137 (Depositor), 0.134 (DCC)
R-Value Observed: 0.139 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.333	α = 90
b = 132.087	β = 90
c = 137.319	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
SHELX	model building
MLPHARE	phasing
DM	model building
SOLVE	phasing
RESOLVE	model building
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
SHELX	phasing
DM	phasing
RESOLVE	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-04-07

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

This entry supersedes: 3K95

Revision History (Full details and data files)

Version 1.0: 2010-04-07
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-08
Changes: Refinement description
Version 2.0: 2021-08-04
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2024-11-20
Changes: Data collection, Database references, Structure summary