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- PDB-3hb8: Structures of Thymidylate Synthase R163K with Substrates and Inhi... -

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Basic information

Entry
Database: PDB / ID: 3hb8
TitleStructures of Thymidylate Synthase R163K with Substrates and Inhibitors Show Subunit Asymmetry
ComponentsThymidylate synthase
KeywordsTRANSFERASE / methyl transferase / Methyltransferase / Nucleotide biosynthesis
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
PHOSPHATE ION / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / Thymidylate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.74 Å
AuthorsGibson, L.M. / Lovelace, L.L. / Lebioda, L.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2011
Title: Structures of human thymidylate synthase R163K with dUMP, FdUMP and glutathione show asymmetric ligand binding.
Authors: Gibson, L.M. / Celeste, L.R. / Lovelace, L.L. / Lebioda, L.
History
DepositionMay 4, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 27, 2013Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.5Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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
E: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,97513
Polymers178,6755
Non-polymers1,3018
Water2,234124
1
A: Thymidylate synthase
B: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,9976
Polymers71,4702
Non-polymers5274
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5740 Å2
ΔGint-26 kcal/mol
Surface area22130 Å2
MethodPISA
2
C: Thymidylate synthase
hetero molecules

C: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0864
Polymers71,4702
Non-polymers6162
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area5480 Å2
ΔGint-32 kcal/mol
Surface area22580 Å2
MethodPISA
3
D: Thymidylate synthase
E: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,9355
Polymers71,4702
Non-polymers4653
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5460 Å2
ΔGint-29 kcal/mol
Surface area22210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)196.459, 122.149, 99.157
Angle α, β, γ (deg.)90.000, 114.550, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Thymidylate synthase / / TSase / TS


Mass: 35734.926 Da / Num. of mol.: 5 / Mutation: R163K
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 / Deoxyuridine monophosphate


Mass: 308.182 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H13N2O8P
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 3.03 Å3/Da / Density % sol: 59.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 10-20% PEG 4000, 20mM BME, 3mM potassium phosphate, 0.1M TRIS, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 19, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.74→50 Å / Num. obs: 52210 / % possible obs: 96.7 % / Redundancy: 3 % / Rmerge(I) obs: 0.069 / Χ2: 2.897 / Net I/σ(I): 28.126
Reflection shellResolution: 2.74→2.84 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.268 / Num. unique all: 4462 / Χ2: 1.201 / % possible all: 82.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
CNSphasing
RefinementResolution: 2.74→50 Å / Occupancy max: 1 / Occupancy min: 0.39 / FOM work R set: 0.781 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.261 5079 9.1 %
Rwork0.21 45096 -
obs-50175 89.5 %
Solvent computationBsol: 28.449 Å2
Displacement parametersBiso max: 117.88 Å2 / Biso mean: 59.982 Å2 / Biso min: 14.81 Å2
Baniso -1Baniso -2Baniso -3
1-19.618 Å20 Å28.128 Å2
2---6.882 Å20 Å2
3----12.736 Å2
Refinement stepCycle: LAST / Resolution: 2.74→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11336 0 82 124 11542
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_d1.262
X-RAY DIFFRACTIONc_mcbond_it1.7052
X-RAY DIFFRACTIONc_scbond_it2.9963
X-RAY DIFFRACTIONc_mcangle_it2.8242.5
X-RAY DIFFRACTIONc_scangle_it4.4053.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 50

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.74-2.76
2.76-2.780.42620.27657
2.78-2.80.332530.318559612
2.8-2.820.379740.341776850
2.82-2.840.371970.325812909
2.84-2.860.457880.351873961
2.86-2.880.406940.356856950
2.88-2.90.417880.359883971
2.9-2.930.3831010.325852953
2.93-2.950.361160.31868984
2.95-2.980.3811090.3249041013
2.98-30.3881030.307888991
3-3.030.388960.3299101006
3.03-3.060.321900.2999641054
3.06-3.090.4631000.309899999
3.09-3.120.438960.2999041000
3.12-3.150.3571220.2949311053
3.15-3.180.3231030.39131016
3.18-3.210.3781040.289871091
3.21-3.250.3471030.2739231026
3.25-3.290.323860.279691055
3.29-3.320.3281160.2699661082
3.32-3.360.2951060.2649251031
3.36-3.410.3131100.26710001110
3.41-3.450.3191000.2579151015
3.45-3.50.2811100.2529961106
3.5-3.550.3111030.2319611064
3.55-3.60.3261020.25510111113
3.6-3.660.3191050.2329601065
3.66-3.720.2681060.2239871093
3.72-3.780.2671010.2159491050
3.78-3.850.3221170.23710021119
3.85-3.930.2511090.2179791088
3.93-4.010.251140.1859691083
4.01-4.090.2061170.1749771094
4.09-4.190.239980.1779841082
4.19-4.290.2141380.169601098
4.29-4.410.1771050.13610031108
4.41-4.540.1821190.1399641083
4.54-4.690.1821240.1329821106
4.69-4.850.1881110.1359981109
4.85-5.050.2221160.169951111
5.05-5.280.2011200.1669891109
5.28-5.560.2421250.189781103
5.56-5.90.2661000.20110071107
5.9-6.360.2631200.2079911111
6.36-70.2511280.1989811109
7-8.010.1851090.14610181127
8.01-10.090.1821270.12810041131
10.09-500.010.212980.1979691067
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramHicupCNS_TOPPAR:protein.topHIcup
X-RAY DIFFRACTION2CNS_TOPPAR:trs.paramCNS_TOPPAR:trs.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top
X-RAY DIFFRACTION5CNS_TOPPAR:dUMP.paramCNS_TOPPAR:dUMP.top

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