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- PDB-2rd8: Human Thymidylate Synthase Stabilized in Active Conformation by R... -

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Basic information

Entry
Database: PDB / ID: 2rd8
TitleHuman Thymidylate Synthase Stabilized in Active Conformation by R163K Mutation: Asymmetry and Reactivity of Cys195
Components(Thymidylate synthase) x 2
KeywordsTRANSFERASE / METHYL TRANSFERASE / 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
BETA-MERCAPTOETHANOL / PHOSPHATE ION / Thymidylate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsGibson, L.M. / Lovelace, L.L. / Lebioda, L.
CitationJournal: Biochemistry / Year: 2008
Title: The R163K Mutant of Human Thymidylate Synthase Is Stabilized in an Active Conformation: Structural Asymmetry and Reactivity of Cysteine 195.
Authors: Gibson, L.M. / Lovelace, L.L. / Lebioda, L.
History
DepositionSep 21, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 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_conn ...database_2 / 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
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)71,8145
Polymers71,5462
Non-polymers2683
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.741, 120.741, 129.771
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Thymidylate synthase / TS / TSase


Mass: 35734.926 Da / Num. of mol.: 1 / Mutation: R163K
Source method: isolated from a genetically manipulated source
Details: CYS at position 195 / Source: (gene. exp.) Homo sapiens (human) / Gene: TYMS, TS / Production host: Escherichia coli (E. coli) / References: UniProt: P04818, thymidylate synthase
#2: Protein Thymidylate synthase


Mass: 35811.039 Da / Num. of mol.: 1 / Mutation: R163K
Source method: isolated from a genetically manipulated source
Details: CME at position 195 / Source: (gene. exp.) Homo sapiens (human) / Gene: TYMS, TS / Production host: Escherichia coli (E. coli) / References: UniProt: P04818, thymidylate synthase
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


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


Mass: 18.015 Da / Num. of mol.: 88 / 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: 3.82 Å3/Da / Density % sol: 67.77 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 10-20% PEG 4000, 3mM potassium phosphate, 20mM 2-mercaptoethanol, 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: 0.97243 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 15, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97243 Å / Relative weight: 1
ReflectionResolution: 2.4→33.8 Å / Num. obs: 30034 / % possible obs: 69.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 4.7 % / Rmerge(I) obs: 0.138 / Χ2: 1.708 / Net I/σ(I): 7.8
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 7.8 / Num. unique all: 651 / Χ2: 0.693 / % possible all: 15.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3data extraction
HKL-2000data collection
HKL-2000data reduction
AMoREphasing
RefinementStarting model: 1HVY

1hvy


Resolution: 2.5→33.8 Å / FOM work R set: 0.774 / Isotropic thermal model: overall / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.271 2711 7.1 %random
Rwork0.228 ---
all-30034 --
obs-26954 70.4 %-
Solvent computationBsol: 25.192 Å2
Displacement parametersBiso mean: 46.036 Å2
Baniso -1Baniso -2Baniso -3
1--10.356 Å2-13.846 Å20 Å2
2---10.356 Å20 Å2
3---20.712 Å2
Refinement stepCycle: LAST / Resolution: 2.5→33.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4566 0 14 88 4668
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.33
X-RAY DIFFRACTIONc_mcbond_it1.7742
X-RAY DIFFRACTIONc_scbond_it3.2483
X-RAY DIFFRACTIONc_mcangle_it2.9772.5
X-RAY DIFFRACTIONc_scangle_it4.8693.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramHicupprotein.topHIcup
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5BME.paramBME.top

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