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- PDB-4irr: Crystal Structure of C.elegans Thymidylate Synthase in Complex wi... -

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Basic information

Entry
Database: PDB / ID: 4irr
TitleCrystal Structure of C.elegans Thymidylate Synthase in Complex with dUMP
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
2,3-DIHYDROXY-1,4-DITHIOBUTANE / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / Thymidylate synthase
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.48 Å
AuthorsWilk, P. / Dowiercial, A. / Banaszak, K. / Jarmula, A. / Rypniewski, W. / Rode, W.
CitationJournal: To be Published
Title: Crystal Structure of C.elegans Thymidylate Synthase in Complex with dUMP
Authors: Wilk, P. / Dowiercial, A. / Banaszak, K. / Jarmula, A. / Rypniewski, W. / Rode, W.
History
DepositionJan 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)72,9458
Polymers71,7122
Non-polymers1,2336
Water6,107339
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6770 Å2
ΔGint-29 kcal/mol
Surface area22870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.091, 135.091, 155.771
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-681-

HOH

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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-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP


Mass: 308.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13N2O8P
#3: Chemical
ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O2S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / 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

Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.1M Bis-Tris pH 7.2, 0.2M NaAcetate, 15% PEG 3350, 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: 2.48→29.2 Å / Num. obs: 57989

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å29.25 Å
Translation2.5 Å29.25 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.48→29.2 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.889 / WRfactor Rfree: 0.2541 / WRfactor Rwork: 0.2244 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8178 / SU B: 5.951 / SU ML: 0.137 / SU R Cruickshank DPI: 0.2257 / SU Rfree: 0.2042 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.226 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2645 2933 5.1 %RANDOM
Rwork0.2318 ---
obs0.2334 57989 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 122.15 Å2 / Biso mean: 38.5893 Å2 / Biso min: 18.86 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å2-0 Å2
2--0.01 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.48→29.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4650 0 72 339 5061
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.024890
X-RAY DIFFRACTIONr_angle_refined_deg1.1531.976620
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5325596
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.44223.924237
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.24215857
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4321534
X-RAY DIFFRACTIONr_chiral_restr0.0750.2709
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213710
LS refinement shellResolution: 2.48→2.549 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 186 -
Rwork0.306 3671 -
all-3857 -
obs--94.86 %

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