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- PDB-7ndz: ThyX reconstituted with N5-carbinolamine flavin -

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Basic information

Entry
Database: PDB / ID: 7ndz
TitleThyX reconstituted with N5-carbinolamine flavin
ComponentsFlavin-dependent thymidylate synthase
KeywordsTRANSFERASE / FLAVIN-DEPENDENT THYMIDYLATE SYNTHASE / METHYLENETETRAHYDROFOLATE
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
Thymidylate synthase ThyX / Thymidylate synthase ThyX superfamily / Thymidylate synthase complementing protein / Flavin-dependent thymidylate synthase (thyX) domain profile.
Similarity search - Domain/homology
DIHYDROFLAVINE-ADENINE DINUCLEOTIDE / Chem-HUF / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Flavin-dependent thymidylate synthase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsBou-Nader, C. / Pecqueur, L. / Hamdane, D.
Funding support France, 3items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-11-IDEX-0004-02 France
Agence Nationale de la Recherche (ANR)ANR-15-CE11-0004-01 France
Agence Nationale de la Recherche (ANR)ANR-11-LABX-0011-01 France
CitationJournal: Nat Commun / Year: 2021
Title: An enzymatic activation of formaldehyde for nucleotide methylation.
Authors: Bou-Nader, C. / Stull, F.W. / Pecqueur, L. / Simon, P. / Guerineau, V. / Royant, A. / Fontecave, M. / Lombard, M. / Palfey, B.A. / Hamdane, D.
History
DepositionFeb 2, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 29, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)113,61111
Polymers110,0154
Non-polymers3,5977
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18100 Å2
ΔGint-53 kcal/mol
Surface area31150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.080, 117.560, 142.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 27503.680 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: thyX, thy1, TM_0449 / Plasmid: pET11d / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9WYT0, thymidylate synthase (FAD)

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Non-polymers , 5 types, 44 molecules

#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-HUF / [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4S)-5-[5-methanoyl-7,8-dimethyl-2,4-bis(oxidanylidene)-1H-benzo[g]pteridin-10-yl]-2,3,4-tris(oxidanyl)pentyl] hydrogen phosphate


Mass: 815.576 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C28H35N9O16P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-FDA / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE


Mass: 787.566 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H35N9O15P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.1 Å3/Da / Density % sol: 41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 200 40% w/v ANAEROBY

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Oct 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.7→40.83 Å / Num. obs: 26019 / % possible obs: 99.48 % / Redundancy: 4.7 % / Biso Wilson estimate: 91.01 Å2 / CC1/2: 0.994 / Rrim(I) all: 0.1826 / Net I/σ(I): 6.02
Reflection shellResolution: 2.7→2.8 Å / Num. unique obs: 2560 / CC1/2: 0.486 / Rrim(I) all: 1.396 / % possible all: 99.92

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSVERSION Jun 1, 2017 BUILT=20170601data reduction
XDSVERSION Jun 1, 2017 BUILT=20170601data scaling
PHASER2.8.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1o24

1o24


Resolution: 2.7→40.83 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.915 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.342
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1294 4.97 %RANDOM
Rwork0.22 ---
obs0.222 26018 99.6 %-
Displacement parametersBiso mean: 73.89 Å2
Baniso -1Baniso -2Baniso -3
1--17.0946 Å20 Å20 Å2
2--7.6613 Å20 Å2
3---9.4333 Å2
Refine analyzeLuzzati coordinate error obs: 0.41 Å
Refinement stepCycle: 1 / Resolution: 2.7→40.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6854 0 242 37 7133
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0087301HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.989965HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2413SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1225HARMONIC5
X-RAY DIFFRACTIONt_it7301HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.53
X-RAY DIFFRACTIONt_other_torsion17.71
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion958SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8375SEMIHARMONIC4
LS refinement shellResolution: 2.7→2.72 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2423 -4.61 %
Rwork0.2388 497 -
all0.239 521 -
obs--99.41 %

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