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- PDB-4fzb: Structure of thymidylate synthase ThyX complexed to a new inhibitor -

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Basic information

Entry
Database: PDB / ID: 4fzb
TitleStructure of thymidylate synthase ThyX complexed to a new inhibitor
ComponentsProbable thymidylate synthase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Homotetramer / FAD-dependent Thymidylate synthase / TRANSFERASE-TRANSFERASE INHIBITOR complex
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
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3070 / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / 2-Layer Sandwich ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3070 / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-0VJ / FLAVIN-ADENINE DINUCLEOTIDE / Probable flavin-dependent thymidylate synthase
Similarity search - Component
Biological speciesParamecium bursaria Chlorella virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsBasta, T. / Boum, Y. / Briffotaux, J. / Becker, H.F. / Lamarre-Jouenne, I. / Lambry, J.C. / Skouloubris, S. / Liebl, U. / van Tilbeurgh, H. / Graille, M. / Myllylkallio, H.
CitationJournal: Open Biology / Year: 2012
Title: Mechanistic and structural basis for inhibition of thymidylate synthase ThyX.
Authors: Basta, T. / Boum, Y. / Briffotaux, J. / Becker, H.F. / Lamarre-Jouenne, I. / Lambry, J.C. / Skouloubris, S. / Liebl, U. / Graille, M. / van Tilbeurgh, H. / Myllykallio, H.
History
DepositionJul 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2013Group: Data collection
Revision 1.2Sep 13, 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: Probable thymidylate synthase
B: Probable thymidylate synthase
C: Probable thymidylate synthase
D: Probable thymidylate synthase
E: Probable thymidylate synthase
F: Probable thymidylate synthase
G: Probable thymidylate synthase
H: Probable thymidylate synthase
I: Probable thymidylate synthase
J: Probable thymidylate synthase
K: Probable thymidylate synthase
L: Probable thymidylate synthase
M: Probable thymidylate synthase
N: Probable thymidylate synthase
O: Probable thymidylate synthase
P: Probable thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)437,69761
Polymers419,40416
Non-polymers18,29345
Water1,65792
1
A: Probable thymidylate synthase
B: Probable thymidylate synthase
C: Probable thymidylate synthase
D: Probable thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,48316
Polymers104,8514
Non-polymers4,63212
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23510 Å2
ΔGint-68 kcal/mol
Surface area30180 Å2
MethodPISA
2
E: Probable thymidylate synthase
F: Probable thymidylate synthase
G: Probable thymidylate synthase
H: Probable thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,48316
Polymers104,8514
Non-polymers4,63212
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23320 Å2
ΔGint-67 kcal/mol
Surface area29740 Å2
MethodPISA
3
I: Probable thymidylate synthase
J: Probable thymidylate synthase
K: Probable thymidylate synthase
L: Probable thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,32714
Polymers104,8514
Non-polymers4,47610
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22500 Å2
ΔGint-75 kcal/mol
Surface area29560 Å2
MethodPISA
4
M: Probable thymidylate synthase
N: Probable thymidylate synthase
O: Probable thymidylate synthase
P: Probable thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,40515
Polymers104,8514
Non-polymers4,55411
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22950 Å2
ΔGint-65 kcal/mol
Surface area29920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.975, 120.585, 128.249
Angle α, β, γ (deg.)111.65, 91.13, 90.18
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Probable thymidylate synthase / TS / TSase


Mass: 26212.752 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paramecium bursaria Chlorella virus 1 / Strain: Paramecium bursaria chlorella virus (PBCV-1) / Gene: A674R, ThyX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O41156, thymidylate synthase (FAD)
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-0VJ / 2-hydroxy-3-(4-methoxybenzyl)naphthalene-1,4-dione


Mass: 294.301 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C18H14O4
#4: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.4 Å3/Da / Density % sol: 48.7 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 10% PEG 5000 MME, 12% isopropanol, 12% DMSO, 100 mM MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K
PH range: 6,5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 10, 2009
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.59→35 Å / Num. all: 120946 / Num. obs: 111996 / % possible obs: 92.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.25 % / Biso Wilson estimate: 61.94 Å2 / Rsym value: 0.069 / Net I/σ(I): 10.7
Reflection shellResolution: 2.59→2.75 Å / Redundancy: 2.25 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.524 / % possible all: 93.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
BUSTER2.8.0refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CFA

2cfa


Resolution: 2.59→34.21 Å / Cor.coef. Fo:Fc: 0.9172 / Cor.coef. Fo:Fc free: 0.8805 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2613 5633 5.03 %RANDOM
Rwork0.2106 ---
all0.2132 120946 --
obs0.2132 111995 --
Displacement parametersBiso mean: 53.73 Å2
Baniso -1Baniso -2Baniso -3
1--5.7276 Å20.516 Å21.5743 Å2
2--11.5469 Å23.2882 Å2
3----5.8193 Å2
Refine analyzeLuzzati coordinate error obs: 0.385 Å
Refinement stepCycle: LAST / Resolution: 2.59→34.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25151 0 1252 92 26495
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0127095HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1936828HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d9470SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes924HARMONIC2
X-RAY DIFFRACTIONt_gen_planes4094HARMONIC5
X-RAY DIFFRACTIONt_it27095HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion2.65
X-RAY DIFFRACTIONt_other_torsion23.18
X-RAY DIFFRACTIONt_improper_torsion144HARMONIC0
X-RAY DIFFRACTIONt_chiral_improper_torsion3493SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact31471SEMIHARMONIC4
LS refinement shellResolution: 2.59→2.66 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 381 5.05 %
Rwork0.2316 7166 -
all0.2344 7547 -

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