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- PDB-9w6x: Crystal Structure of YtkW in Complex with SAM -

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Basic information

Entry
Database: PDB / ID: 9w6x
TitleCrystal Structure of YtkW in Complex with SAM
ComponentsYtkW
KeywordsTRANSFERASE / YtkW / SAM
Function / homologyMethyltransferase domain 25 / Methyltransferase domain / methyltransferase activity / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / S-ADENOSYLMETHIONINE / YtkW
Function and homology information
Biological speciesStreptomyces sp. TP-A2060 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsWang, S.C. / Pan, L.F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)92253301 China
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2026
Title: S-Methyl Thioester Formation Uncovers Early Biosynthetic Steps of Yatakemycin.
Authors: Feng, J. / Wang, S. / Yang, X. / Tian, T. / Huang, W. / Teng, X. / Pan, H.X. / Sun, A. / Pu, J. / Pan, L. / Tang, G.L.
History
DepositionAug 5, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 15, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: YtkW
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8972
Polymers21,4981
Non-polymers3981
Water72140
1
A: YtkW
hetero molecules

A: YtkW
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7944
Polymers42,9972
Non-polymers7972
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_445-x-1,-y-1,z1
Buried area1720 Å2
ΔGint-17 kcal/mol
Surface area15990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.799, 63.799, 238.440
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2

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Components

#1: Protein YtkW


Mass: 21498.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. TP-A2060 (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I3NN71
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.71 Å3/Da / Density % sol: 54.6 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 1 M succinic acid-sodium hydroxide(pH 7.0)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Apr 6, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.38→61.63 Å / Num. obs: 10418 / % possible obs: 100 % / Redundancy: 12.4 % / Biso Wilson estimate: 47.2 Å2 / CC1/2: 0.995 / Net I/σ(I): 12.1
Reflection shellResolution: 2.38→2.42 Å / Num. unique obs: 485 / CC1/2: 0.643

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.38→38.2 Å / SU ML: 0.2982 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.7449
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2503 517 4.97 %
Rwork0.1971 9880 -
obs0.1996 10397 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.17 Å2
Refinement stepCycle: LAST / Resolution: 2.38→38.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1502 0 27 40 1569
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00271564
X-RAY DIFFRACTIONf_angle_d0.6382130
X-RAY DIFFRACTIONf_chiral_restr0.042244
X-RAY DIFFRACTIONf_plane_restr0.0047275
X-RAY DIFFRACTIONf_dihedral_angle_d11.3735230
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.38-2.620.33591210.27952386X-RAY DIFFRACTION100
2.62-2.990.33741300.2652422X-RAY DIFFRACTION99.84
3-3.770.27111320.20862471X-RAY DIFFRACTION100
3.77-38.20.20071340.15952601X-RAY DIFFRACTION99.6
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.37290738737-1.727951656418.402936435672.67024931525-0.3807208022179.128700161050.532093716162-2.42217706512-2.681259333640.752207775701-0.1611351714190.5822051131641.99513041776-1.549453112060.384346302641.51211259915-0.453908398817-0.2978333642310.06845949760910.1362076344710.643384559273-23.8215355261-31.6933679419-8.52437017104
22.67431743291.149855460421.044769737312.330717364331.168655989436.907985240470.2827113959260.0478192433305-0.127714265391-0.1449873726250.313623346682-0.1771807500340.6114336844830.719722678741-0.5420167239330.4257137605730.0103954195106-0.03441006405760.349480747116-0.1060199031970.409385282663-11.5345038044-18.3774408089-16.5684137138
34.065491358731.81850120502-5.095738514746.66675380971-2.90746713786.841646719730.0239368587119-0.623427550534-0.6196769465850.262601054540.273337745964-0.2587561948350.2049481168350.765053415002-0.4718014054450.347518449893-0.0532815465873-0.07187745958920.479933537093-0.1706613548350.321621374996-11.8227917482-17.8159768958-7.92472217194
43.22413803778-1.51855789102-0.4343860238691.98009442033-0.4836271503949.140555572430.25682166509-0.2646686678960.1114171066030.03183128022230.4569548172210.255517977762-0.314796026873-2.27016382699-0.5397964103660.4175875507280.03827076781070.05187432131750.8165185489390.2568196457520.471122367991-27.2034595945-13.7646386293-14.8815039857
53.36785862455-1.37598385291-1.106087792759.008430105152.74328337986.188970334830.01014926828540.1395420951660.3151464990690.5843884982550.7032268834550.3498765945030.243107395055-1.38314688943-0.5141169098480.4695935325890.0647608688226-0.00449226087910.7851992980880.2362659966360.410536649937-24.9238256294-15.781336648-24.8201605174
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 20 )1 - 201 - 20
22chain 'A' and (resid 21 through 86 )21 - 8621 - 86
33chain 'A' and (resid 87 through 100 )87 - 10087 - 100
44chain 'A' and (resid 101 through 170 )101 - 170101 - 170
55chain 'A' and (resid 171 through 199 )171 - 199171 - 199

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