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- PDB-9iqc: Monooxygenase dependent on riboflavin with dCMP and FAD -

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Basic information

Entry
Database: PDB / ID: 9iqc
TitleMonooxygenase dependent on riboflavin with dCMP and FAD
ComponentsThymidylate synthase
KeywordsHYDROLASE / complex / FAD / Monooxygenase
Function / homology
Function and homology information


thymidylate synthase activity / dTMP biosynthetic process / methylation
Similarity search - Function
Thymidylate synthase/dCMP hydroxymethylase / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase/dCMP hydroxymethylase superfamily / Thymidylate synthase
Similarity search - Domain/homology
2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE / FLAVIN-ADENINE DINUCLEOTIDE / Thymidylate synthase
Similarity search - Component
Biological speciesPhage #D (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsYu, H. / Lianrong, W.
Funding support China, 1items
OrganizationGrant numberCountry
Not funded China
CitationJournal: To Be Published
Title: structure of XAN60475 at 1.69 Angstroms resolution
Authors: Yu, H.
History
DepositionJul 12, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3303
Polymers27,2371
Non-polymers1,0932
Water5,549308
1
A: Thymidylate synthase
hetero molecules

A: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6596
Polymers54,4742
Non-polymers2,1854
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation10_554-y,-x,-z-1/61
Buried area6370 Å2
ΔGint-19 kcal/mol
Surface area18710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.702, 64.702, 230.362
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)

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Components

#1: Protein Thymidylate synthase / Flavin-dependent monooxygenase


Mass: 27236.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phage #D (virus) / Strain: HY126 / Gene: 308Ecol101PP_00194 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0AA50FDD6
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-DCM / 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE


Mass: 307.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N3O7P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.56 Å3/Da / Density % sol: 51.86 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 8% v/v Tacsimate pH 6.0 20% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 6, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.69→56.03 Å / Num. obs: 32844 / % possible obs: 99.8 % / Redundancy: 12.6 % / CC1/2: 1 / Rmerge(I) obs: 0.116 / Net I/σ(I): 25
Reflection shellResolution: 1.69→1.78 Å / Num. unique obs: 32844 / CC1/2: 0.918 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
PHENIXphasing
PROCORdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.69→56.03 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / Phase error: 19.6053
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1926 1995 6.07 %
Rwork0.1741 30845 -
obs0.1752 32840 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.73 Å2
Refinement stepCycle: LAST / Resolution: 1.69→56.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1882 0 73 308 2263
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00572005
X-RAY DIFFRACTIONf_angle_d0.85272725
X-RAY DIFFRACTIONf_chiral_restr0.0552291
X-RAY DIFFRACTIONf_plane_restr0.0072342
X-RAY DIFFRACTIONf_dihedral_angle_d12.775718
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.69-1.730.31421330.29342072X-RAY DIFFRACTION97.09
1.73-1.780.29861400.27772142X-RAY DIFFRACTION98.87
1.78-1.830.23311380.23132144X-RAY DIFFRACTION99.74
1.83-1.890.22171400.20072161X-RAY DIFFRACTION99.7
1.89-1.960.22511400.17992178X-RAY DIFFRACTION99.57
1.96-2.040.19631400.17052153X-RAY DIFFRACTION99.7
2.04-2.130.24471410.17762163X-RAY DIFFRACTION99.96
2.13-2.240.19571410.17442193X-RAY DIFFRACTION99.91
2.24-2.390.20261410.1632191X-RAY DIFFRACTION99.79
2.39-2.570.18571420.16432206X-RAY DIFFRACTION99.96
2.57-2.830.19011450.17042223X-RAY DIFFRACTION100
2.83-3.240.17121460.16582259X-RAY DIFFRACTION99.96
3.24-4.080.15611480.15182289X-RAY DIFFRACTION100
4.08-56.030.18251600.16722471X-RAY DIFFRACTION99.89

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