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- PDB-9ir2: phage HY126 hydroxylase AfhB with cofactor FMN and substrate dCMP -

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Basic information

Entry
Database: PDB / ID: 9ir2
Titlephage HY126 hydroxylase AfhB with cofactor FMN and substrate dCMP
ComponentsThymidylate synthase
KeywordsHYDROLASE / COMPLEX / hydroxylase / FMN
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 MONONUCLEOTIDE / Thymidylate synthase
Similarity search - Component
Biological speciesPhage #D (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.31 Å
AuthorsYu, H. / Lianrong, W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: STRUCTURE of protein XAN60475 at 1.31 angstroms resolution
Authors: Yu, H.
History
DepositionJul 13, 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)28,0934
Polymers27,2371
Non-polymers8563
Water5,477304
1
A: Thymidylate synthase
hetero molecules

A: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1858
Polymers54,4742
Non-polymers1,7116
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation10_554-y,-x,-z-1/61
Buried area8360 Å2
ΔGint-24 kcal/mol
Surface area17540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.600, 64.600, 230.210
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)
Components on special symmetry positions
IDModelComponents
11A-448-

HOH

21A-644-

HOH

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Components

#1: Protein Thymidylate synthase / protein XAN60475


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


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / 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: 2.55 Å3/Da / Density % sol: 51.68 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Ammonium citrate dibasic 20% w/v Polyethyele 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: Jun 8, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.31→50.32 Å / Num. obs: 66855 / % possible obs: 96.2 % / Redundancy: 28.6 % / CC1/2: 1 / Rmerge(I) obs: 0.063 / Net I/σ(I): 32.8
Reflection shellResolution: 1.31→1.34 Å / Rmerge(I) obs: 0.931 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3365 / CC1/2: 0.85

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XSCALEdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.31→50.32 Å / SU ML: 0.1353 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.7583
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1795 1996 3 %
Rwork0.1548 64648 -
obs0.1556 66644 95.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.93 Å2
Refinement stepCycle: LAST / Resolution: 1.31→50.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1882 0 57 304 2243
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00491985
X-RAY DIFFRACTIONf_angle_d0.86092691
X-RAY DIFFRACTIONf_chiral_restr0.0811287
X-RAY DIFFRACTIONf_plane_restr0.0068341
X-RAY DIFFRACTIONf_dihedral_angle_d13.8823723
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.31-1.340.3116970.2743113X-RAY DIFFRACTION65.93
1.34-1.380.27871220.24393923X-RAY DIFFRACTION83.21
1.38-1.420.25671370.22084436X-RAY DIFFRACTION94.5
1.42-1.470.22791430.19154707X-RAY DIFFRACTION99.2
1.47-1.520.18761450.16254696X-RAY DIFFRACTION99.63
1.52-1.580.18281470.13794735X-RAY DIFFRACTION99.78
1.58-1.650.17441460.13274759X-RAY DIFFRACTION99.88
1.65-1.740.18331470.14294754X-RAY DIFFRACTION99.88
1.74-1.850.19461470.15174790X-RAY DIFFRACTION99.98
1.85-1.990.17861490.14634789X-RAY DIFFRACTION99.98
1.99-2.190.17941490.14334848X-RAY DIFFRACTION99.98
2.19-2.510.16241510.14314869X-RAY DIFFRACTION100
2.51-3.160.15191530.15274950X-RAY DIFFRACTION100
3.16-50.320.18011630.15475279X-RAY DIFFRACTION99.96

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