3KOM | pdb_00003kom

Crystal structure of apo transketolase from Francisella tularensis

PDB DOI: https://doi.org/10.2210/pdb3KOM/pdb

Classification: TRANSFERASE
Organism(s): Francisella tularensis subsp. tularensis SCHU S4
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2009-11-13 Released: 2009-12-01
Deposition Author(s): Anderson, S.M., Wawrzak, Z., Skarina, T., Gordon, E., Kwon, K., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.199 (Depositor), 0.221 (DCC)
R-Value Work:
0.163 (Depositor), 0.193 (DCC)
R-Value Observed:
0.165 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3KOM

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of apo transketolase from Francisella tularensis

Anderson, S.M., Wawrzak, Z., Skarina, T., Gordon, E., Kwon, K., Savchenko, A., Anderson, W.F.

To be published.

Macromolecule Content

Total Structure Weight: 148.81 kDa
Atom Count: 11,675
Modeled Residue Count: 1,302
Deposited Residue Count: 1,326
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transketolase	A, B	663	Francisella tularensis subsp. tularensis SCHU S4	Mutation(s): 1 Gene Names: tktA, FTT1369c, FTT_1369c EC: 2.2.1.1
UniProt
Find proteins for Q5NF74 (Francisella tularensis subsp. tularensis (strain SCHU S4 / Schu 4)) Explore Q5NF74 Go to UniProtKB: Q5NF74
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5NF74
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET
OCS Query on OCS	A, B	L-PEPTIDE LINKING	C₃ H₇ N O₅ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.199 (Depositor), 0.221 (DCC)
R-Value Work: 0.163 (Depositor), 0.193 (DCC)
R-Value Observed: 0.165 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.49	α = 90
b = 109.29	β = 90
c = 128.56	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
BLU-MAX	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CRANK	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-12-01

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2009-12-01
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Source and taxonomy, Version format compliance
Version 1.2: 2011-12-14
Changes: Structure summary
Version 1.3: 2017-11-01
Changes: Refinement description
Version 1.4: 2021-10-13
Changes: Database references, Derived calculations

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.