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- PDB-4up1: Crystal structure of native human Thymidylate synthase in active form -

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Basic information

Entry
Database: PDB / ID: 4up1
TitleCrystal structure of native human Thymidylate synthase in active form
ComponentsTHYMIDYLATE SYNTHASE
KeywordsTRANSFERASE / LOW-SALT CONDITIONS
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 / negative regulation of translation / mitochondrial inner membrane / 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
Thymidylate synthase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.991 Å
AuthorsDeschamps, P. / Rety, S. / Leulliot, N.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2017
Title: Crystal structure of the active form of native human thymidylate synthase in the absence of bound substrates.
Authors: Deschamps, P. / Rety, S. / Bareille, J. / Leulliot, N.
History
DepositionJun 11, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jun 21, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

Downloads & links

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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)144,26916
Polymers143,1164
Non-polymers1,15312
Water00
1
A: THYMIDYLATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1635
Polymers35,7791
Non-polymers3844
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: THYMIDYLATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2596
Polymers35,7791
Non-polymers4805
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: THYMIDYLATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9713
Polymers35,7791
Non-polymers1922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: THYMIDYLATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8752
Polymers35,7791
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.790, 106.460, 101.500
Angle α, β, γ (deg.)90.00, 108.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
THYMIDYLATE SYNTHASE / TS / TSASE


Mass: 35778.980 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA 2 / References: UniProt: P04818, thymidylate synthase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4

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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: 3.29 Å3/Da / Density % sol: 62.6 % / Description: NONE
Crystal growDetails: 25% PEG 4000 30MM AMMONIUM SULFATE 20MM B-MERCAPTOETHANOL 100MM TRIS-HCL PH 9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97627
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 5, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97627 Å / Relative weight: 1
ReflectionResolution: 2.99→46.55 Å / Num. obs: 34338 / % possible obs: 91.7 % / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Biso Wilson estimate: 68.9 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.11
Reflection shellResolution: 2.99→3.1 Å / Redundancy: 2 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 1.75 / % possible all: 65

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YPV

1ypv


Resolution: 2.991→46.55 Å / SU ML: 0.36 / σ(F): 1.37 / Phase error: 27.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2444 1717 5 %
Rwork0.2141 --
obs0.2156 34332 91.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 74.9 Å2
Refinement stepCycle: LAST / Resolution: 2.991→46.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9131 0 60 0 9191
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039419
X-RAY DIFFRACTIONf_angle_d0.77312750
X-RAY DIFFRACTIONf_dihedral_angle_d13.3453520
X-RAY DIFFRACTIONf_chiral_restr0.0331333
X-RAY DIFFRACTIONf_plane_restr0.0031650
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9914-3.07940.3224990.32721883X-RAY DIFFRACTION64
3.0794-3.17870.36171170.32822228X-RAY DIFFRACTION75
3.1787-3.29230.33581410.3032669X-RAY DIFFRACTION91
3.2923-3.42410.33041530.28732919X-RAY DIFFRACTION99
3.4241-3.57990.33051530.27092895X-RAY DIFFRACTION98
3.5799-3.76850.26821510.24332884X-RAY DIFFRACTION98
3.7685-4.00450.24431530.23052894X-RAY DIFFRACTION98
4.0045-4.31350.21351510.20492884X-RAY DIFFRACTION98
4.3135-4.74720.22451520.1692888X-RAY DIFFRACTION97
4.7472-5.43330.2211520.17732885X-RAY DIFFRACTION97
5.4333-6.84190.21651490.20262823X-RAY DIFFRACTION95
6.8419-46.55550.18521460.1612763X-RAY DIFFRACTION91

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