7FGQ | pdb_00007fgq

Crystal structure of Thymidylate kinase with TMP and its low-resolution (SAXS) solution structure from Brugia malayi

PDB DOI: https://doi.org/10.2210/pdb7FGQ/pdb

Classification: TRANSFERASE
Organism(s): Brugia malayi
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-07-27 Released: 2022-07-27
Deposition Author(s): Ramachandran, R., Vishwakarma, J., Sharma, V.K.
Funding Organization(s): Council of Scientific & Industrial Research (CSIR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.91 Å
R-Value Free:
0.249 (Depositor), 0.250 (DCC)
R-Value Work:
0.220 (Depositor), 0.220 (DCC)
R-Value Observed:
0.221 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of Thymidylate kinase with TMP and its low-resolution (SAXS) solution structure from Brugia malayi

Ramachandran, R., Vishwakarma, J., Sharma, V.K.

To be published.

Macromolecule Content

Total Structure Weight: 28.73 kDa
Atom Count: 1,596
Modeled Residue Count: 190
Deposited Residue Count: 252
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
dTMP kinase	A	252	Brugia malayi	Mutation(s): 0 Gene Names: Bm5401, Bm1_23075, BM_Bm5401 EC: 2.7.4.9
UniProt
Find proteins for A0A1P6BP23 (Brugia malayi) Explore A0A1P6BP23 Go to UniProtKB: A0A1P6BP23
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1P6BP23
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TMP (Subject of Investigation/LOI) Query on TMP 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]	THYMIDINE-5'-PHOSPHATE C₁₀ H₁₅ N₂ O₈ P GYOZYWVXFNDGLU-XLPZGREQSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.91 Å
R-Value Free: 0.249 (Depositor), 0.250 (DCC)
R-Value Work: 0.220 (Depositor), 0.220 (DCC)
R-Value Observed: 0.221 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.67	α = 90
b = 58.67	β = 90
c = 119.61	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-07-27

Deposition Author(s):

Ramachandran, R.

Vishwakarma, J.

Funding Organization	Location	Grant Number
Council of Scientific & Industrial Research (CSIR)	India	--

Revision History (Full details and data files)

Version 1.0: 2022-07-27
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description

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.