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- PDB-9iqu: phage HY126 dCMP hydroxylase-AfhB with sustrate dCMP -

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Basic information

Entry
Database: PDB / ID: 9iqu
Titlephage HY126 dCMP hydroxylase-AfhB with sustrate dCMP
ComponentsThymidylate synthase
KeywordsHYDROLASE / COMPLEX / dCMP
Function / homologyThymidylate synthase/dCMP hydroxymethylase / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase/dCMP hydroxymethylase superfamily / Thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / methylation / 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE / Thymidylate synthase
Function and homology information
Biological speciesPhage #D (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsYu, H. / Lianrong, W.
Funding support China, 1items
OrganizationGrant numberCountry
Not funded China
CitationJournal: To Be Published
Title: STRUCTURE OF protein XAN60475 at 1.1.96 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)27,1813
Polymers26,7811
Non-polymers3992
Water5,044280
1
A: Thymidylate synthase
hetero molecules

A: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3616
Polymers53,5632
Non-polymers7994
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation10_554-y,-x,-z-1/61
Buried area6640 Å2
ΔGint-15 kcal/mol
Surface area16890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.190, 65.190, 231.933
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-408-

HOH

21A-572-

HOH

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Components

#1: Protein Thymidylate synthase


Mass: 26781.377 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 coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0AA50FDD6
#2: 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
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / 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: 2.58 Å3/Da / Density % sol: 52.38 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Ammonium acetate;0.1M Sodium acetate teihydrate pH4.6;15% peg 4000

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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 13, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.96→54.85 Å / Num. obs: 20631 / % possible obs: 98 % / Redundancy: 8 % / CC1/2: 0.999 / Net I/σ(I): 28.8
Reflection shellResolution: 1.96→2.06 Å / Rmerge(I) obs: 0.281 / Num. unique obs: 1022 / CC1/2: 0.985

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
PHENIXphasing
autoPROCdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→35.84 Å / SU ML: 0.1713 / Cross valid method: FREE R-VALUE / σ(F): 0.05 / Phase error: 20.4751
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2193 1899 9.2 %RANDOM
Rwork0.1964 18732 --
obs0.1985 20631 93.27 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.07 Å2
Refinement stepCycle: LAST / Resolution: 1.96→35.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1756 0 26 280 2062
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01481822
X-RAY DIFFRACTIONf_angle_d1.27682463
X-RAY DIFFRACTIONf_chiral_restr0.0676264
X-RAY DIFFRACTIONf_plane_restr0.0076316
X-RAY DIFFRACTIONf_dihedral_angle_d7.7405243
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-20.2404990.21351022X-RAY DIFFRACTION73.36
2-2.060.29861160.20141149X-RAY DIFFRACTION82.73
2.06-2.120.22631310.20241262X-RAY DIFFRACTION90.75
2.12-2.190.25161330.21011335X-RAY DIFFRACTION94.83
2.19-2.270.41061200.38211099X-RAY DIFFRACTION79.67
2.27-2.360.24081230.241265X-RAY DIFFRACTION89.26
2.36-2.460.23931390.1871383X-RAY DIFFRACTION98.13
2.46-2.590.2391410.1841378X-RAY DIFFRACTION97.75
2.59-2.760.20541430.18771407X-RAY DIFFRACTION99.04
2.76-2.970.2211460.19671437X-RAY DIFFRACTION99.31
2.97-3.270.18141440.181438X-RAY DIFFRACTION99.81
3.27-3.740.20241470.17971449X-RAY DIFFRACTION99.69
3.74-4.710.16561510.15081494X-RAY DIFFRACTION99.7
4.71-35.840.18621660.18341614X-RAY DIFFRACTION99.72
Refinement TLS params.Method: refined / Origin x: 24.6066437266 Å / Origin y: -24.287597715 Å / Origin z: -10.9969377102 Å
111213212223313233
T0.112516117262 Å20.00596266340572 Å20.00350098546773 Å2-0.103173456515 Å20.00932893068784 Å2--0.0987942734007 Å2
L0.596400604205 °20.0857840567035 °2-0.106155004208 °2-0.435915695642 °2-0.241118939054 °2--0.643073519003 °2
S-0.00184632759065 Å °-0.0547350764322 Å °-0.0470408857944 Å °0.0213495234699 Å °0.0121170053855 Å °0.00232410474049 Å °0.110985423631 Å °-0.0240825810021 Å °-0.000275685161712 Å °
Refinement TLS groupSelection details: all

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