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- PDB-4iqb: High Resolution Crystal Structure of C.elegans Thymidylate Synthase -

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Basic information

Entry
Database: PDB / ID: 4iqb
TitleHigh Resolution Crystal Structure of C.elegans Thymidylate Synthase
ComponentsThymidylate synthase
KeywordsTRANSFERASE / PROTEIN DIMER / DEOXYNUCLEOTIDE BIOSYNTHESIS
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, active site / Thymidylate synthase active site. / Thymidylate synthase / Thymidylate synthase/dCMP hydroxymethylase / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase/dCMP hydroxymethylase superfamily / Thymidylate synthase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Thymidylate synthase
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.13 Å
AuthorsWilk, P. / Dowiercial, A. / Banaszak, K. / Jarmula, A. / Rypniewski, W. / Rode, W.
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: Jarmula, A. / Wilk, P. / Maj, P. / Ludwiczak, J. / Dowiercial, A. / Banaszak, K. / Rypniewski, W. / Ciesla, J. / Dabrowska, M. / Fraczyk, T. / Bronowska, A.K. / Jakowiecki, J. / Filipek, S. / Rode, W.
History
DepositionJan 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2018Group: Data collection / 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 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)71,9044
Polymers71,7122
Non-polymers1922
Water16,970942
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-44 kcal/mol
Surface area23990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.335, 98.367, 69.159
Angle α, β, γ (deg.)90.000, 111.770, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Thymidylate synthase


Mass: 35855.902 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Plasmid: pPIGDM4+stop / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y052, thymidylate synthase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 942 / 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: 2.19 Å3/Da / Density % sol: 43.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1M MES pH 5.6, 0.15M (NH4)2SO4, 18% PEG 5000MME, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorDate: Dec 2, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.13→29.3 Å / Num. obs: 228161
Reflection shellResolution: 1.13→1.15 Å / % possible obs: 89.4 % / Rmerge(I) obs: 0.439 / Mean I/σ(I) obs: 2.01

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å29.35 Å
Translation2.5 Å29.35 Å

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Processing

Software
NameVersionClassificationNB
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.13→29.3 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.978 / WRfactor Rfree: 0.143 / WRfactor Rwork: 0.1168 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.9392 / SU B: 0.731 / SU ML: 0.016 / SU R Cruickshank DPI: 0.0249 / SU Rfree: 0.0264 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.025 / ESU R Free: 0.026 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1387 11419 5 %RANDOM
Rwork0.1135 ---
obs0.1147 228161 99.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 152.2 Å2 / Biso mean: 16.7316 Å2 / Biso min: 5.93 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0 Å2-0.02 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.13→29.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4616 0 10 942 5568
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.025164
X-RAY DIFFRACTIONr_bond_other_d0.0010.023634
X-RAY DIFFRACTIONr_angle_refined_deg2.1941.9647079
X-RAY DIFFRACTIONr_angle_other_deg1.2138907
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7845697
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.1223.611252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.62315958
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8291541
X-RAY DIFFRACTIONr_chiral_restr0.1440.2762
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0215855
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021102
X-RAY DIFFRACTIONr_rigid_bond_restr6.80438797
X-RAY DIFFRACTIONr_sphericity_free40.7055199
X-RAY DIFFRACTIONr_sphericity_bonded11.66159362
LS refinement shellResolution: 1.13→1.158 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 710 -
Rwork0.255 14292 -
all-15002 -
obs--89.45 %

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