3KGB | pdb_00003kgb

Crystal structure of thymidylate synthase 1/2 from Encephalitozoon cuniculi at 2.2 A resolution

PDB DOI: https://doi.org/10.2210/pdb3KGB/pdb

Classification: TRANSFERASE
Organism(s): Encephalitozoon cuniculi GB-M1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-10-28 Released: 2009-11-10
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.246 (Depositor), 0.238 (DCC)
R-Value Work:
0.205 (Depositor), 0.199 (DCC)
R-Value Observed:
0.207 (Depositor)

Starting Model: experimental
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This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of thymidylate synthase 1/2 from Encephalitozoon cuniculi at 2.2 A resolution

Seattle Structural Genomics Center for Infectious Disease (SSGCID), Abendroth, J., Edwards, T.E., Staker, B.

To be published.

Macromolecule Content

Total Structure Weight: 33.19 kDa
Atom Count: 2,099
Modeled Residue Count: 254
Deposited Residue Count: 294
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidylate synthase 1/2	A	294	Encephalitozoon cuniculi GB-M1	Mutation(s): 0 Gene Names: TS-1, ECU01_0180, TS-2, ECU01_1430 EC: 2.1.1.45
UniProt
Find proteins for O62584 (Encephalitozoon cuniculi (strain GB-M1)) Explore O62584 Go to UniProtKB: O62584
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O62584
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.246 (Depositor), 0.238 (DCC)
R-Value Work: 0.205 (Depositor), 0.199 (DCC)
R-Value Observed: 0.207 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.63	α = 90
b = 72.28	β = 90
c = 61.68	γ = 90

Software Package:

Software Name	Purpose
StructureStudio	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-11-10

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2009-11-10
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Refinement description, Source and taxonomy, Version format compliance
Version 1.2: 2018-01-24
Changes: Database references
Version 1.3: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description

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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.