3BHL | pdb_00003bhl

E.coli thymidylate synthase complexes with 5-NO2dUMP and tetrahydrofolate at 1.4 A resolution

PDB DOI: https://doi.org/10.2210/pdb3BHL/pdb

Classification: TRANSFERASE
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-11-28 Released: 2008-12-02
Deposition Author(s): Roberts, S.A., Montfort, W.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free:
0.203 (Depositor), 0.207 (DCC)
R-Value Work:
0.174 (Depositor), 0.181 (DCC)
R-Value Observed:
0.176 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structural Studies of Early Events in Catalysis by Thymidylate Synthase

Arendall III, W.B., Hyatt, D.C., Roberts, S.A., Weichsel, A., Dahlgren, A.L., Maley, F., Montfort, W.R.

To be published.

Macromolecule Content

Total Structure Weight: 63.01 kDa
Atom Count: 5,010
Modeled Residue Count: 528
Deposited Residue Count: 528
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidylate synthase	A, B	264	Escherichia coli	Mutation(s): 0 Gene Names: thyA EC: 2.1.1.45
UniProt
Find proteins for P0A884 (Escherichia coli (strain K12)) Explore P0A884 Go to UniProtKB: P0A884
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A884
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
THG Query on THG Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain D [auth A] MOL2 format, chain H [auth B] MOL2 format, chain D [auth A] mmCIF format, chain H [auth B] mmCIF format, chain D [auth A]	D [auth A], H [auth B]	(6S)-5,6,7,8-TETRAHYDROFOLATE C₁₉ H₂₃ N₇ O₆ MSTNYGQPCMXVAQ-RYUDHWBXSA-N		Interactions Focus chain D [auth A] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B]
NDU Query on NDU Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain C [auth A] MOL2 format, chain G [auth B] MOL2 format, chain C [auth A] mmCIF format, chain G [auth B] mmCIF format, chain C [auth A]	C [auth A], G [auth B]	2'-DEOXY-5-NITROURIDINE 5'-MONOPHOSPHATE C₉ H₁₄ N₃ O₁₀ P ZYBJIJYGXJSDTC-XZBKPIIZSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], I [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B]

Modified Residues 1 Unique
ID	Chains	Modified Residue	Modification Type	Formula	2D Diagram
CXM Query on CXM	A, B	MET	Carboxylation	C₆ H₁₁ N O₄ S

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.203 (Depositor), 0.207 (DCC)
R-Value Work: 0.174 (Depositor), 0.181 (DCC)
R-Value Observed: 0.176 (Depositor)

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.87	α = 90
b = 124.87	β = 90
c = 66.394	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2008-12-02

Deposition Author(s):

Roberts, S.A.

Montfort, W.R.

Revision History (Full details and data files)

Version 1.0: 2008-12-02
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-11-13
Changes: Structure summary