6AUJ | pdb_00006auj

Crystal structure of thymidylate synthase from Elizabethkingia anophelis NUHP1

PDB DOI: https://doi.org/10.2210/pdb6AUJ/pdb

Classification: TRANSFERASE
Organism(s): Elizabethkingia anophelis NUHP1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-09-01 Released: 2017-09-27
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.176 (Depositor), 0.176 (DCC)
R-Value Work:
0.157 (Depositor), 0.158 (DCC)
R-Value Observed:
0.158 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 2.0 of the entry. See complete history.

Literature

Crystal structure of thymidylate synthase from Elizabethkingia anophelis NUHP1

Mayclin, S.J., Delker, S.L., Lorimer, D.D., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 94.21 kDa
Atom Count: 6,632
Modeled Residue Count: 757
Deposited Residue Count: 816
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidylate synthase	A, B, C	272	Elizabethkingia anophelis NUHP1	Mutation(s): 0 Gene Names: thyA, BD94_0762 EC: 2.1.1.45
UniProt
Find proteins for A0A077EAN3 (Elizabethkingia anophelis NUHP1) Explore A0A077EAN3 Go to UniProtKB: A0A077EAN3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A077EAN3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain F [auth C] SDF format, chain E [auth B] SDF format, chain D [auth A] MOL2 format, chain F [auth C] MOL2 format, chain E [auth B] MOL2 format, chain D [auth A] mmCIF format, chain F [auth C] mmCIF format, chain E [auth B] mmCIF format, chain D [auth A]	D [auth A], E [auth B], F [auth C]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
M0H Query on M0H	A, B, C	L-PEPTIDE LINKING	C₄ H₉ N O₃ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.176 (Depositor), 0.176 (DCC)
R-Value Work: 0.157 (Depositor), 0.158 (DCC)
R-Value Observed: 0.158 (Depositor)

Diffraction Data:

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.11	α = 90
b = 78.55	β = 90.49
c = 73.37	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Coot	model building

Structure Validation

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Entry History

Deposition Data

Released Date: 2017-09-27

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2017-09-27
Type: Initial release
Version 1.1: 2023-10-04
Changes: Data collection, Database references, Refinement description
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection, 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.