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- PDB-5noo: Crystal Structure of C.elegans Thymidylate Synthase in Complex wi... -

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Basic information

Entry
Database: PDB / ID: 5noo
TitleCrystal Structure of C.elegans Thymidylate Synthase in Complex with dUMP and Tomudex
ComponentsThymidylate synthase
KeywordsTRANSFERASE / enzyme / nematode / complex
Function / homology
Function and homology information


thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / methylation
Similarity search - Function
Thymidylate Synthase; Chain A / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase/dCMP hydroxymethylase / Thymidylate synthase, active site / Thymidylate synthase active site. / Thymidylate synthase / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase/dCMP hydroxymethylase superfamily / Thymidylate synthase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
TOMUDEX / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / Thymidylate synthase
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsWilk, P. / Jarmula, A. / Maj, P. / Dowiercial, A. / Banaszak, K. / Rypniewski, W. / Rode, W.
Funding support Poland, 2items
OrganizationGrant numberCountry
Ministry of Science and Higher EducationN301 3948 33 Poland
National Science Centre2011/01/B/NZ6/01781 Poland
CitationJournal: J. Mol. Graph. Model. / Year: 2017
Title: Crystal structures of nematode (parasitic T. spiralis and free living C. elegans), compared to mammalian, thymidylate synthases (TS). Molecular docking and molecular dynamics simulations in ...Title: Crystal structures of nematode (parasitic T. spiralis and free living C. elegans), compared to mammalian, thymidylate synthases (TS). Molecular docking and molecular dynamics simulations in search for nematode-specific inhibitors of TS.
Authors: Jarmua, A. / Wilk, P. / Maj, P. / Ludwiczak, J. / Dowiercia, A. / Banaszak, K. / Rypniewski, W. / Ciesla, J. / Dabrowska, M. / Fraczyk, T. / Bronowska, A.K. / Jakowiecki, J. / Filipek, S. / Rode, W.
History
DepositionApr 12, 2017Deposition site: PDBE / Processing site: PDBE
SupersessionMay 3, 2017ID: 4IQQ
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thymidylate synthase
B: Thymidylate synthase
C: Thymidylate synthase
D: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,49012
Polymers143,4244
Non-polymers3,0678
Water1,51384
1
A: Thymidylate synthase
B: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,2456
Polymers71,7122
Non-polymers1,5334
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7160 Å2
ΔGint-27 kcal/mol
Surface area23190 Å2
MethodPISA
2
C: Thymidylate synthase
D: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,2456
Polymers71,7122
Non-polymers1,5334
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6750 Å2
ΔGint-27 kcal/mol
Surface area22860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.085, 94.314, 122.048
Angle α, β, γ (deg.)90.000, 105.360, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Thymidylate synthase /


Mass: 35855.902 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y052, thymidylate synthase
#2: Chemical
ChemComp-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP / Deoxyuridine monophosphate


Mass: 308.182 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C9H13N2O8P / References: thymidylate synthase
#3: Chemical
ChemComp-D16 / TOMUDEX / ZD1694 / Raltitrexed / Raltitrexed


Mass: 458.488 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H22N4O6S / Comment: chemotherapy, inhibitor*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.65 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.1M Bis-Tris pH 7.0, 0.2M NaAcetate, 17% PEG 3350

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION NOVA / Wavelength: 1.5418 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: Dec 3, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→14.7 Å / Num. obs: 32822 / % possible obs: 96.4 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.135 / Net I/σ(I): 4.6
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.375 / Num. unique all: 4929 / Rsym value: 0.375 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.11.1-2575refinement
PDB_EXTRACT3.22data extraction
CrysalisPro1.171.36.20data reduction
CrysalisPro1.171.36.20data collection
PHASER2.3.0phasing
SCALA3.3.20data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EB4

4eb4


Resolution: 2.9→14.7 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2473 --
Rwork0.2102 --
obs-32808 96.01 %
Displacement parametersBiso max: 158.43 Å2 / Biso mean: 41.6245 Å2 / Biso min: 8.07 Å2
Refinement stepCycle: LAST / Resolution: 2.9→14.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9163 0 208 84 9455
LS refinement shellResolution: 2.9→2.9847 Å
RfactorNum. reflection% reflection
Rfree0.3362 129 -
Rwork0.3029 2645 -
obs--99.1 %

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