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- PDB-3n5g: Crystal Structure of histidine-tagged human thymidylate synthase -

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Basic information

Entry
Database: PDB / ID: 3n5g
TitleCrystal Structure of histidine-tagged human thymidylate synthase
ComponentsThymidylate synthase
KeywordsTRANSFERASE / peptide inhibitor / protein-peptide complex / interface inhibitor
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 / response to vitamin A / thymidylate synthase / 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 / response to vitamin A / thymidylate synthase / 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 progesterone / response to cytokine / 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 / cytosol / cytoplasm
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
Thymidylate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsPozzi, C. / Cardinale, D. / Guaitoli, G. / Tondi, D. / Luciani, R. / Myllykallio, H. / Ferrari, S. / Costi, M.P. / Mangani, S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Protein-protein interface-binding peptides inhibit the cancer therapy target human thymidylate synthase.
Authors: Cardinale, D. / Guaitoli, G. / Tondi, D. / Luciani, R. / Henrich, S. / Salo-Ahen, O.M. / Ferrari, S. / Marverti, G. / Guerrieri, D. / Ligabue, A. / Frassineti, C. / Pozzi, C. / Mangani, S. / ...Authors: Cardinale, D. / Guaitoli, G. / Tondi, D. / Luciani, R. / Henrich, S. / Salo-Ahen, O.M. / Ferrari, S. / Marverti, G. / Guerrieri, D. / Ligabue, A. / Frassineti, C. / Pozzi, C. / Mangani, S. / Fessas, D. / Guerrini, R. / Ponterini, G. / Wade, R.C. / Costi, M.P.
History
DepositionMay 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 24, 2013Group: Database references
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6714
Polymers37,3831
Non-polymers2883
Water2,684149
1
A: Thymidylate synthase
hetero molecules

A: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,3428
Polymers74,7662
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area5300 Å2
ΔGint-98 kcal/mol
Surface area22190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.070, 96.070, 83.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Thymidylate synthase / / TSase / TS


Mass: 37382.848 Da / Num. of mol.: 1
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-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.96 Å3/Da / Density % sol: 58.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: 30% saturated Ammonium Sulfate + 20mM BME + 0.1M TRIS pH8.3, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 20, 2008
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.27→41.6 Å / Num. obs: 20905 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 10.8 % / Biso Wilson estimate: 39.8 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 26
Reflection shellResolution: 2.27→2.39 Å / Redundancy: 11 % / Rmerge(I) obs: 0.351 / Mean I/σ(I) obs: 7.1 / Num. unique all: 2988 / Rsym value: 0.351 / % possible all: 100

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YPV

1ypv


Resolution: 2.27→41.6 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.942 / SU B: 8.679 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.179 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20149 1069 5.1 %RANDOM
Rwork0.16622 ---
obs0.16808 19806 99.98 %-
all-20905 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.509 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refine analyze
FreeObs
Luzzati sigma a0.16 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2.27→41.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2140 0 15 149 2304
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0222207
X-RAY DIFFRACTIONr_angle_refined_deg1.8991.9792982
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.465261
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.77523.333105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.36715378
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0361517
X-RAY DIFFRACTIONr_chiral_restr0.1440.2313
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211667
X-RAY DIFFRACTIONr_mcbond_it1.151.51309
X-RAY DIFFRACTIONr_mcangle_it2.18422116
X-RAY DIFFRACTIONr_scbond_it3.5033898
X-RAY DIFFRACTIONr_scangle_it5.3674.5866
LS refinement shellResolution: 2.27→2.329 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.202 83 -
Rwork0.191 1431 -
obs-1431 100 %
Refinement TLS params.Method: refined / Origin x: 49.3003 Å / Origin y: -7.7524 Å / Origin z: 15.8894 Å
111213212223313233
T0.1607 Å20.0356 Å2-0.0262 Å2-0.0244 Å2-0.0258 Å2--0.0911 Å2
L0.9558 °2-0.3419 °20.0681 °2-1.4364 °20.3984 °2--1.34 °2
S0.1788 Å °0.1257 Å °-0.1594 Å °-0.1485 Å °-0.061 Å °0.0399 Å °0.03 Å °-0.0633 Å °-0.1178 Å °

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