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

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Basic information

Entry
Database: PDB / ID: 2rda
TitleHuman Thymidylate Synthase Stabilized in Active Conformation by R163K Mutation: Asymmetry and Reactivity of Cys195
ComponentsThymidylate synthase
KeywordsTRANSFERASE / methyl transferase / asymmetric / Methyltransferase / Nucleotide biosynthesis
Function / homology
Function and homology information


uracil metabolic process / intestinal epithelial cell maturation / response to folic acid / Interconversion of nucleotide di- and triphosphates / thymidylate synthase / sequence-specific mRNA binding / response to vitamin A / tetrahydrofolate interconversion / thymidylate synthase activity / cartilage development ...uracil metabolic process / intestinal epithelial cell maturation / response to folic acid / Interconversion of nucleotide di- and triphosphates / thymidylate synthase / sequence-specific mRNA binding / response to vitamin A / tetrahydrofolate interconversion / thymidylate synthase activity / cartilage development / folic acid binding / dTMP biosynthetic process / dTTP biosynthetic process / DNA biosynthetic process / G1/S-Specific Transcription / developmental growth / response to glucocorticoid / response to cytokine / mRNA regulatory element binding translation repressor activity / response to progesterone / 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, 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: 2.67 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 1.0Jun 10, 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_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 1.4Aug 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
C: Thymidylate synthase
D: Thymidylate synthase
E: Thymidylate synthase
F: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,04113
Polymers214,4106
Non-polymers6317
Water3,279182
1
A: Thymidylate synthase
B: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,5653
Polymers71,4702
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-26.1 kcal/mol
Surface area23140 Å2
MethodPISA
2
C: Thymidylate synthase
hetero molecules

C: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,8166
Polymers71,4702
Non-polymers3464
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area5370 Å2
ΔGint-36.3 kcal/mol
Surface area22760 Å2
MethodPISA
3
D: Thymidylate synthase
hetero molecules

D: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,6604
Polymers71,4702
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Buried area4920 Å2
ΔGint-29.3 kcal/mol
Surface area22540 Å2
MethodPISA
4
E: Thymidylate synthase
F: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,7385
Polymers71,4702
Non-polymers2683
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5060 Å2
ΔGint-35.3 kcal/mol
Surface area23260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.794, 123.794, 284.766
Angle α, β, γ (deg.)90.00, 90.00, 120.00
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.: 6 / Mutation: R163K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TYMS, TS / Production host: Escherichia coli (E. coli) / References: UniProt: P04818, thymidylate synthase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.94 Å3/Da / Density % sol: 58.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 10-20% PEG 4K, 3mM KPi, 20mM BME, 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-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 24, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.67→50 Å / Num. obs: 72672 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 7.1 % / Rmerge(I) obs: 0.207 / Net I/σ(I): 15.5
Reflection shellResolution: 2.67→2.77 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.647 / Mean I/σ(I) obs: 15.5 / % possible all: 94.9

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Processing

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

1hvy


Resolution: 2.67→107.21 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.876 / SU B: 11.572 / SU ML: 0.244 / Cross valid method: THROUGHOUT / ESU R: 0.621 / ESU R Free: 0.348 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27947 3559 5 %RANDOM
Rwork0.20856 ---
obs0.21215 67080 97.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.228 Å2
Baniso -1Baniso -2Baniso -3
1--1.67 Å2-0.83 Å20 Å2
2---1.67 Å20 Å2
3---2.5 Å2
Refinement stepCycle: LAST / Resolution: 2.67→107.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13619 0 33 182 13834
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0380.02214005
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg3.061.96218949
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.18651681
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.52823.401685
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.027152397
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.20515109
X-RAY DIFFRACTIONr_chiral_restr0.1920.21987
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0210765
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2950.26541
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3550.29340
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2220.2649
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.220.292
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.20.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7741.58722
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.927213533
X-RAY DIFFRACTIONr_scbond_it4.23336171
X-RAY DIFFRACTIONr_scangle_it6.2584.55416
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.67→2.739 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.402 248 -
Rwork0.305 4813 -
obs--95.15 %

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