3HYL | pdb_00003hyl

Crystal Structure of Transketolase from Bacillus anthracis

PDB DOI: https://doi.org/10.2210/pdb3HYL/pdb

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

Deposited: 2009-06-22 Released: 2009-06-30
Deposition Author(s): Maltseva, N., Kim, Y., Kwon, K., Joachimiak, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.16 Å
R-Value Free:
0.230 (Depositor), 0.228 (DCC)
R-Value Work:
0.176 (Depositor), 0.173 (DCC)
R-Value Observed:
0.178 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of Transketolase from Bacillus anthracis

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

To be published.

Macromolecule Content

Total Structure Weight: 153.91 kDa
Atom Count: 10,868
Modeled Residue Count: 1,326
Deposited Residue Count: 1,380
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 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: BAA_3769, 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A6L7H165
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain Q [auth B] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain J [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain J [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain J [auth A]	J [auth A], M [auth A], N [auth A], Q [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain Q [auth B] Interactions & Density Focus chain J [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain Q [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain S [auth B] MOL2 format, chain S [auth B] mmCIF format, chain S [auth B]	S [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain S [auth B] Interactions & Density Focus chain S [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain W [auth B] SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain W [auth B] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain W [auth B] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], O [auth B], P [auth B], T [auth B], U [auth B], V [auth B], W [auth B]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A] mmCIF format, chain L [auth A]	L [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain K [auth A] MOL2 format, chain R [auth B] MOL2 format, chain K [auth A] mmCIF format, chain R [auth B] mmCIF format, chain K [auth A]	K [auth A], R [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain R [auth B] Interactions & Density Focus chain K [auth A] Focus chain R [auth B]

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: 2.16 Å
R-Value Free: 0.230 (Depositor), 0.228 (DCC)
R-Value Work: 0.176 (Depositor), 0.173 (DCC)
R-Value Observed: 0.178 (Depositor)

Diffraction Data: https://doi.org/10.18430/m33hyl

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 138.801	α = 90
b = 70.975	β = 117.35
c = 145.795	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

Entry History

Deposition Data

Released Date: 2009-06-30

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2009-06-30
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2024-11-27
Changes: Data collection, Database references, Derived calculations, Structure summary