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- PDB-8gxo: The crystal structure of CsFAOMT1 in complex with SAH -

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Basic information

Entry
Database: PDB / ID: 8gxo
TitleThe crystal structure of CsFAOMT1 in complex with SAH
ComponentsCaffeoyl-CoA O-methyltransferase
KeywordsTRANSFERASE / CsFAOMT1 / SAH / O-methyltransferase
Function / homologycaffeoyl-CoA O-methyltransferase activity / lignin biosynthetic process / O-methyltransferase / Class I-like SAM-dependent O-methyltransferase / SAM-dependent O-methyltransferase class I-type profile. / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / S-ADENOSYL-L-HOMOCYSTEINE / Caffeoyl-CoA O-methyltransferase
Function and homology information
Biological speciesCamellia sinensis (black tea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsZhang, Z.M. / Zhou, Y.E. / Huang, H.S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2023
Title: Characterization of two O-methyltransferases involved in the biosynthesis of O-methylated catechins in tea plant.
Authors: Jin, J.Q. / Qu, F.R. / Huang, H. / Liu, Q.S. / Wei, M.Y. / Zhou, Y. / Huang, K.L. / Cui, Z. / Chen, J.D. / Dai, W.D. / Zhu, L. / Yao, M.Z. / Zhang, Z.M. / Chen, L.
History
DepositionSep 20, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 13, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Caffeoyl-CoA O-methyltransferase
B: Caffeoyl-CoA O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3355
Polymers53,5422
Non-polymers7933
Water9,116506
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-31 kcal/mol
Surface area17760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.899, 99.899, 99.030
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein Caffeoyl-CoA O-methyltransferase / / CsFAOMT1


Mass: 26770.787 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camellia sinensis (black tea) / Gene: HYC85_015345 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A7J7GXF2, caffeoyl-CoA O-methyltransferase
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 506 / Source method: isolated from a natural source / Formula: H2O
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: 2.78 Å3/Da / Density % sol: 55.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.05 M Cadmium Sulfate hydrate, 0.1 M HEPES pH 7.5, 1.0 M Sodium Acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CAMD / Beamline: GCPCC / Wavelength: 0.97869 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Dec 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97869 Å / Relative weight: 1
ReflectionResolution: 1.74→50 Å / Num. obs: 53776 / % possible obs: 99 % / Redundancy: 20 % / Biso Wilson estimate: 26.06 Å2 / CC1/2: 1 / Net I/σ(I): 23.8
Reflection shellResolution: 1.74→1.83 Å / Num. unique obs: 847 / CC1/2: 0.855

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3C3Y

3c3y


Resolution: 1.74→43.26 Å / SU ML: 0.1844 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.7012
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2205 2003 3.72 %
Rwork0.1856 51773 -
obs0.1869 53776 90.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.19 Å2
Refinement stepCycle: LAST / Resolution: 1.74→43.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3440 0 53 506 3999
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00683559
X-RAY DIFFRACTIONf_angle_d1.01584819
X-RAY DIFFRACTIONf_chiral_restr0.0577558
X-RAY DIFFRACTIONf_plane_restr0.0079608
X-RAY DIFFRACTIONf_dihedral_angle_d11.4676494
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.780.28631540.23844030X-RAY DIFFRACTION100
1.78-1.830.26191550.21114053X-RAY DIFFRACTION100
1.83-1.880.27341620.22034040X-RAY DIFFRACTION100
1.88-1.940.3475680.23681778X-RAY DIFFRACTION44.24
1.94-2.010.21061580.19854063X-RAY DIFFRACTION100
2.01-2.090.22351130.19132965X-RAY DIFFRACTION73.08
2.09-2.190.23481560.20024051X-RAY DIFFRACTION100
2.19-2.30.22521240.18923221X-RAY DIFFRACTION79.34
2.3-2.450.25631590.20564062X-RAY DIFFRACTION100
2.45-2.630.26651610.19654088X-RAY DIFFRACTION100
2.63-2.90.26181270.20633199X-RAY DIFFRACTION78.44
2.9-3.320.23011560.17924133X-RAY DIFFRACTION100
3.32-4.180.17341440.16043805X-RAY DIFFRACTION91.84
4.18-43.260.19151660.17314285X-RAY DIFFRACTION99.66

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