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- PDB-3gg5: Replacement of Val3 in Human Thymidylate Synthase Affects Its Kin... -

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Basic information

Entry
Database: PDB / ID: 3gg5
TitleReplacement of Val3 in Human Thymidylate Synthase Affects Its Kinetic Properties and Intracellular Stability
ComponentsThymidylate synthase
KeywordsTRANSFERASE / Methyltransferase / Nucleotide biosynthesis
Function / homology
Function and homology information


thymidylate synthase / Interconversion of nucleotide di- and triphosphates / sequence-specific mRNA binding / folic acid binding / thymidylate synthase activity / tetrahydrofolate interconversion / dTMP biosynthetic process / dTTP biosynthetic process / DNA biosynthetic process / G1/S-Specific Transcription ...thymidylate synthase / Interconversion of nucleotide di- and triphosphates / sequence-specific mRNA binding / folic acid binding / thymidylate synthase activity / tetrahydrofolate interconversion / dTMP biosynthetic process / dTTP biosynthetic process / DNA biosynthetic process / G1/S-Specific Transcription / mRNA regulatory element binding translation repressor activity / methylation / mitochondrial inner membrane / negative regulation of translation / mitochondrial matrix / mitochondrion / nucleus / cytoplasm / cytosol
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
PHOSPHATE ION / Thymidylate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.77 Å
AuthorsHuang, X. / Gibson, L.M. / Bell, B.J. / Lovelace, L.L. / Lebioda, L.
CitationJournal: Biochemistry / Year: 2010
Title: Replacement of Val3 in human thymidylate synthase affects its kinetic properties and intracellular stability .
Authors: Huang, X. / Gibson, L.M. / Bell, B.J. / Lovelace, L.L. / Pena, M.M. / Berger, F.G. / Berger, S.H. / Lebioda, L.
History
DepositionFeb 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 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 1.3Oct 20, 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 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)143,6908
Polymers143,3084
Non-polymers3824
Water41423
1
A: Thymidylate synthase
B: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,8454
Polymers71,6542
Non-polymers1912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4940 Å2
ΔGint-43 kcal/mol
Surface area22690 Å2
MethodPISA
2
C: Thymidylate synthase
D: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,8454
Polymers71,6542
Non-polymers1912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5050 Å2
ΔGint-44 kcal/mol
Surface area23330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.562, 94.864, 130.864
Angle α, β, γ (deg.)90.00, 122.43, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Thymidylate synthase / TSase / TS


Mass: 35826.980 Da / Num. of mol.: 4 / Mutation: V3Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OK/SW-cl.29, TS, TYMS / Plasmid: PTSO80 / Production host: Escherichia coli (E. coli) / Strain (production host): TX61- / References: UniProt: P04818, thymidylate synthase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


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


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.88 Å3/Da / Density % sol: 57.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Tris,PH8.0, 30mM ammonium sulfate, 24%PEG4000, 20mM BME , VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 4, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 36191 / % possible obs: 88.2 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 10.572
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.537 / % possible all: 67

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.006data extraction
HKL-3000data collection
HKL-2000data reduction
CNSphasing
RefinementResolution: 2.77→50 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.254 2631 8.8 %
Rwork0.237 --
obs0.237 26568 89.3 %
Solvent computationBsol: 46.245 Å2
Displacement parametersBiso mean: 64.86 Å2
Baniso -1Baniso -2Baniso -3
1--17.559 Å20 Å24.667 Å2
2--14.92 Å20 Å2
3---2.638 Å2
Refinement stepCycle: LAST / Resolution: 2.77→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9131 0 20 23 9174
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.053
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d4.453
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.1532.5
X-RAY DIFFRACTIONc_mcangle_it3.6213
X-RAY DIFFRACTIONc_scbond_it2.6863
X-RAY DIFFRACTIONc_scangle_it4.1563.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top
X-RAY DIFFRACTION5CNS_TOPPAR:fdump.paramCNS_TOPPAR:fdump.top

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