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- PDB-4kar: Crystal structure of FDTS (TM0449) mutant (H53D) with FAD -

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Basic information

Entry
Database: PDB / ID: 4kar
TitleCrystal structure of FDTS (TM0449) mutant (H53D) with FAD
ComponentsThymidylate synthase
KeywordsTRANSFERASE / thyX / FDTS / H53D mutant / FAD / Novel FDTS fold / Convertion of dUMP to dTMP using Tetrahydrofolate / and NAD(P)H
Function / homology
Function and homology information


thymidylate synthase (FAD) / thymidylate synthase (FAD) activity / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / NADPH binding / flavin adenine dinucleotide binding / methylation
Similarity search - Function
Gyrase A; domain 2 - #170 / Thymidylate synthase ThyX / Thymidylate synthase ThyX superfamily / Thymidylate synthase complementing protein / Flavin-dependent thymidylate synthase (thyX) domain profile. / Gyrase A; domain 2 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Flavin-dependent thymidylate synthase
Similarity search - Component
Biological speciesThermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.03 Å
AuthorsMathews, I.I.
CitationJournal: J Bioterror Biodef / Year: 2013
Title: Flavin-Dependent Thymidylate Synthase as a Drug Target for Deadly Microbes: Mutational Study and a Strategy for Inhibitor Design.
Authors: Mathews, I.I.
History
DepositionApr 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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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)113,4799
Polymers109,9224
Non-polymers3,5575
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19510 Å2
ΔGint-77 kcal/mol
Surface area34280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.990, 116.640, 141.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.960394, 0.237306, -0.146045), (0.255421, 0.54026, -0.801797), (-0.111369, -0.807344, -0.579476)73.20985, 103.0862, 220.43663
3given(0.958497, -0.242193, 0.150417), (-0.240243, -0.970209, -0.031281), (0.153512, -0.006154, -0.988128)-5.58037, 97.3858, 223.4657
4given(-0.999835, -0.006015, -0.017141), (-0.010654, -0.570105, 0.821503), (-0.014714, 0.82155, 0.569947)70.38229, -25.79089, 14.33943

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Components

#1: Protein
Thymidylate synthase / TS / TSase


Mass: 27480.621 Da / Num. of mol.: 4 / Fragment: TM0449 (unp residues 1-220) / Mutation: H53D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: thy1, thyX, tm0449, TM_0449 / Plasmid: pMH1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WYT0, 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-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.02 Å3/Da / Density % sol: 39.26 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 50 - 60% PEG200, 0.1Tris.HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 23, 2004 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.03→38.2 Å / Num. all: 58450 / Num. obs: 58450 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 20.1
Reflection shellResolution: 2.03→2.08 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.881 / Mean I/σ(I) obs: 1.87 / Num. unique all: 4269 / % possible all: 99.2

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Processing

Software
NameVersionClassification
Blu-Icedata collection
REFMACrefinement
XDSpackagedata reduction
XDSpackagedata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: pdb entry 1O26

1o26


Resolution: 2.03→38.15 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.939 / SU B: 5.859 / SU ML: 0.155 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.22 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24876 2923 5 %RANDOM
Rwork0.19528 ---
obs0.19801 55525 99.76 %-
all-58450 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.451 Å2
Baniso -1Baniso -2Baniso -3
1-4.91 Å20 Å20 Å2
2---1.55 Å20 Å2
3----3.36 Å2
Refinement stepCycle: LAST / Resolution: 2.03→38.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7198 0 153 150 7501
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0197575
X-RAY DIFFRACTIONr_bond_other_d0.0010.027149
X-RAY DIFFRACTIONr_angle_refined_deg1.5711.97110265
X-RAY DIFFRACTIONr_angle_other_deg0.843316395
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6065853
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.99222.467381
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.129151293
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2481569
X-RAY DIFFRACTIONr_chiral_restr0.0980.21096
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218262
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021885
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.03→2.083 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 213 -
Rwork0.323 4037 -
obs--99.16 %

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