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- PDB-5x67: Human thymidylate synthase in complex with dUMP and nolatrexed -

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Basic information

Entry
Database: PDB / ID: 5x67
TitleHuman thymidylate synthase in complex with dUMP and nolatrexed
ComponentsThymidylate synthase
KeywordsTRANSFERASE / methyltransferase
Function / homology
Function and homology information


uracil metabolic process / response to organophosphorus / intestinal epithelial cell maturation / response to folic acid / Interconversion of nucleotide di- and triphosphates / thymidylate synthase / response to vitamin A / sequence-specific mRNA binding / cartilage development / tetrahydrofolate interconversion ...uracil metabolic process / response to organophosphorus / intestinal epithelial cell maturation / response to folic acid / Interconversion of nucleotide di- and triphosphates / thymidylate synthase / response to vitamin A / sequence-specific mRNA binding / cartilage development / tetrahydrofolate interconversion / thymidylate synthase activity / folic acid binding / dTMP biosynthetic process / dTTP biosynthetic process / DNA biosynthetic process / G1/S-Specific Transcription / developmental growth / dihydrofolate reductase activity / response to glucocorticoid / mRNA regulatory element binding translation repressor activity / response to cytokine / response to progesterone / liver regeneration / response to toxic substance / circadian rhythm / methylation / response to ethanol / mitochondrial inner membrane / negative regulation of translation / mitochondrial matrix / response to xenobiotic stimulus / protein homodimerization activity / mitochondrion / nucleus / cytoplasm / cytosol
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
Chem-7Z9 / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / Thymidylate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsChen, D. / Jansson, A. / Larsson, A. / Nordlund, P.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Nanyang Technological UniversityM060080004.70301200 Singapore
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Structural analyses of human thymidylate synthase reveal a site that may control conformational switching between active and inactive states.
Authors: Chen, D. / Jansson, A. / Sim, D. / Larsson, A. / Nordlund, P.
History
DepositionFeb 21, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)67,6936
Polymers66,5082
Non-polymers1,1854
Water4,810267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5660 Å2
ΔGint-27 kcal/mol
Surface area21240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.290, 108.290, 106.034
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122

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Components

#1: Protein Thymidylate synthase / TSase


Mass: 33254.125 Da / Num. of mol.: 2 / Fragment: UNP residues 26-313
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TYMS, TS, OK/SW-cl.29 / Production host: Escherichia coli (E. coli) / References: UniProt: P04818, thymidylate synthase
#2: Chemical ChemComp-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP


Mass: 308.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13N2O8P
#3: Chemical ChemComp-7Z9 / 2-azanyl-6-methyl-5-pyridin-4-ylsulfanyl-3H-quinazolin-4-one / Nolatrexed / 2-Amino-6-methyl-5-(4-pyridylthio)-1H-quinazolin-4-one


Mass: 284.336 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H12N4OS / Comment: inhibitor*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.35 Å3/Da / Density % sol: 47.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 100mM sodium calcodylate, pH 6.5, 25% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1.013 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.013 Å / Relative weight: 1
ReflectionResolution: 2.13→48.22 Å / Num. obs: 35533 / % possible obs: 99.5 % / Redundancy: 15.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.177 / Rpim(I) all: 0.046 / Rrim(I) all: 0.183 / Net I/σ(I): 15.5 / Num. measured all: 560607 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.13-2.2150.8674084727180.8730.2280.8974.394.4
9.06-48.2212.40.04269085550.9990.0120.04337.299.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
Aimless0.2.14data scaling
PDB_EXTRACT3.22data extraction
XDSdata processing
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1I00

1i00


Resolution: 2.13→48.22 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.924 / SU B: 4.108 / SU ML: 0.108 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.198 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2065 1693 4.8 %RANDOM
Rwork0.1535 ---
obs0.156 33804 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 75.81 Å2 / Biso mean: 22.127 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å20 Å20 Å2
2---0.52 Å20 Å2
3---1.04 Å2
Refinement stepCycle: final / Resolution: 2.13→48.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4593 0 80 267 4940
Biso mean--14.91 28.81 -
Num. residues----574
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0194805
X-RAY DIFFRACTIONr_bond_other_d0.0020.024496
X-RAY DIFFRACTIONr_angle_refined_deg1.8741.9786516
X-RAY DIFFRACTIONr_angle_other_deg1.041310327
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2855574
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.69523.392227
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.35215798
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.551536
X-RAY DIFFRACTIONr_chiral_restr0.1160.2686
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0215409
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021159
LS refinement shellResolution: 2.135→2.19 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.225 106 -
Rwork0.19 2320 -
all-2426 -
obs--93.92 %

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