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- PDB-5chp: T. maritima ThyX in complex with TyC5-03 -

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Basic information

Entry
Database: PDB / ID: 5chp
TitleT. maritima ThyX in complex with TyC5-03
ComponentsThymidylate synthase ThyX
KeywordsHYDROLASE / ThyX in complex with inhibitor
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
Chem-51Q / FLAVIN-ADENINE DINUCLEOTIDE / Flavin-dependent thymidylate synthase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSurade, S. / Luciani, R. / Saxena, P. / Santucci, M. / Ferrari, S. / Venturelli, A. / Marverti, G. / Ponterini, G. / Abell, C.A. / Blundell, T.L. / Costi, M.P.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
EU FP6 United Kingdom
CitationJournal: To Be Published
Title: Identification of inhibitors targeting substrate-binding site in Mycobacterium tuberculosis FAD-dependent Thymidylate synthase (ThyX) through Virtual Screening: A New study de-fining the ...Title: Identification of inhibitors targeting substrate-binding site in Mycobacterium tuberculosis FAD-dependent Thymidylate synthase (ThyX) through Virtual Screening: A New study de-fining the binding mechanism of Inhibitors
Authors: Surade, S.
History
DepositionJul 10, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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

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Assembly

Deposited unit
A: Thymidylate synthase ThyX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7813
Polymers27,7781
Non-polymers1,0032
Water4,053225
1
A: Thymidylate synthase ThyX
hetero molecules

A: Thymidylate synthase ThyX
hetero molecules

A: Thymidylate synthase ThyX
hetero molecules

A: Thymidylate synthase ThyX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,12312
Polymers111,1124
Non-polymers4,0118
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
crystal symmetry operation10_555-x,-y,z1
crystal symmetry operation15_555y,x,-z1
Buried area21480 Å2
ΔGint-70 kcal/mol
Surface area32910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.580, 110.580, 122.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
SymmetryPoint symmetry: (Schoenflies symbol: D2 (2x2 fold dihedral))

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Components

#1: Protein Thymidylate synthase ThyX / TSase


Mass: 27777.994 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: thyX, thy1, TM_0449 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9WYT0, thymidylate synthase (FAD)
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-51Q / (2S)-2-[(3-hydroxy-5-oxo-4,5-dihydro-1,2,4-triazin-6-yl)sulfanyl]propanoic acid / TyC5-03


Mass: 217.202 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H7N3O4S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.38 Å3/Da / Density % sol: 63.64 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: Hanging drop, soaking regrown crystal with the organic compound
PH range: 6.0-7.5 / Temp details: 16 degrees celcius

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.7→31.56 Å / Num. obs: 39623 / % possible obs: 99.74 % / Redundancy: 6.2 % / Net I/σ(I): 20

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KQ4

1kq4


Resolution: 1.7→30.74 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.371 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2005 2104 5 %RANDOM
Rwork0.1698 ---
obs0.17131 39622 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.685 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2---0.05 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.7→30.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1817 0 67 225 2109
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.021953
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.5761.992650
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3635218
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.44522.42195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.06215331
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0031517
X-RAY DIFFRACTIONr_chiral_restr0.2170.2277
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0211478
X-RAY DIFFRACTIONr_gen_planes_other
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_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.703→1.747 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 143 -
Rwork0.269 2639 -
obs--97.14 %

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