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- PDB-6j61: Crystal Structure of Thymidylate Synthase, Thy1, from Thermus the... -

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Basic information

Entry
Database: PDB / ID: 6j61
TitleCrystal Structure of Thymidylate Synthase, Thy1, from Thermus thermophilus having an Extra C Terminal Domain
ComponentsFlavin-dependent thymidylate synthase
KeywordsTRANSFERASE / Thymidylate synthase / pyrimidine nucleotide biosynthetic pathway / C-terminal domain / Structural Genomics
Function / homology
Function and homology information


thymidylate synthase (FAD) / thymidylate synthase (FAD) activity / dTMP biosynthetic process / dTTP biosynthetic process / flavin adenine dinucleotide binding / methylation
Similarity search - Function
Thymidylate synthase ThyX / Thymidylate synthase ThyX superfamily / Thymidylate synthase complementing protein / Flavin-dependent thymidylate synthase (thyX) domain profile.
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / PHOSPHATE ION / Flavin-dependent thymidylate synthase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsOgawa, A. / Sampei, G. / Kawai, G.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2019
Title: Crystal structure of the flavin-dependent thymidylate synthase Thy1 from Thermus thermophilus with an extra C-terminal domain.
Authors: Ogawa, A. / Sampei, G. / Kawai, G.
History
DepositionJan 12, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2019Group: Data collection / Database references / Category: citation_author / Item: _citation_author.name
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Flavin-dependent thymidylate synthase
B: Flavin-dependent thymidylate synthase
C: Flavin-dependent thymidylate synthase
D: Flavin-dependent thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,11316
Polymers124,2114
Non-polymers3,90212
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28060 Å2
ΔGint-191 kcal/mol
Surface area35630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.027, 68.362, 134.083
Angle α, β, γ (deg.)90.00, 115.12, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Flavin-dependent thymidylate synthase / FDTS / FAD-dependent thymidylate synthase / Thymidylate synthase ThyX / TSase


Mass: 31052.869 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / Gene: thyX, TTHA1096 / Plasmid: pET-11a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5SJB8, thymidylate synthase (FAD)
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.41 Å3/Da / Density % sol: 48.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 50% 2-Ethoxyethanol, 0.1 M Na/K Phosphate (pH6.2)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Dec 6, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 79925 / % possible obs: 99.7 % / Redundancy: 3.7 % / Biso Wilson estimate: 24.4 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 16.97
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 1.77 / Num. unique obs: 7835 / % possible all: 98.4

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Processing

Software
NameVersionClassification
CNS1.3refinement
HKL-20001.97.9data reduction
HKL-20001.97.7data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1O2B

1o2b


Resolution: 2.5→49.37 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 367087.33 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.279 7335 9.8 %RANDOM
Rwork0.223 ---
obs0.223 74813 93.3 %-
Solvent computationBsol: 56.61 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso mean: 49.5 Å2
Baniso -1Baniso -2Baniso -3
1--8.29 Å20 Å2-2.75 Å2
2--17.56 Å20 Å2
3----9.27 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.46 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.5→49.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7920 0 252 72 8244
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.231.5
X-RAY DIFFRACTIONc_mcangle_it2.042
X-RAY DIFFRACTIONc_scbond_it1.922
X-RAY DIFFRACTIONc_scangle_it2.892.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.362 1012 9 %
Rwork0.309 10240 -
obs--84.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR/PROTEIN_REP.PARAMCNS_TOPPAR/PROTEIN.TOP
X-RAY DIFFRACTION2CNS_TOPPAR/WATER_REP.PARAMCNS_TOPPAR/WATER.TOP
X-RAY DIFFRACTION3CNS_TOPPAR/ION.PARAMCNS_TOPPAR/ION.TOP
X-RAY DIFFRACTION4CNS_TOPPAR/FAD.PARAMFAD.TOP

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