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- PDB-8gxn: The crystal structure of CsFAOMT2 in complex with SAH -

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Basic information

Entry
Database: PDB / ID: 8gxn
TitleThe crystal structure of CsFAOMT2 in complex with SAH
Componentscaffeyl-CoA-O-methyltransferase
KeywordsTRANSFERASE / CsFAOMT2 / SAH / O-methyltransferases
Function / homologyS-ADENOSYL-L-HOMOCYSTEINE
Function and homology information
Biological speciesTheaceae (tea family)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 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 20, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: caffeyl-CoA-O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0383
Polymers26,6291
Non-polymers4092
Water4,882271
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-8 kcal/mol
Surface area11270 Å2
MethodPISA
2
B: caffeyl-CoA-O-methyltransferase
hetero molecules

B: caffeyl-CoA-O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0756
Polymers53,2582
Non-polymers8174
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_557-x,-x+y,-z+7/31
Buried area4130 Å2
ΔGint-46 kcal/mol
Surface area18610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.688, 74.688, 81.523
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11B-457-

HOH

21B-555-

HOH

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Components

#1: Protein caffeyl-CoA-O-methyltransferase


Mass: 26628.857 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Theaceae (tea family) / Production host: Escherichia alba (bacteria)
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / 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


Mass: 18.015 Da / Num. of mol.: 271 / 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: 2.44 Å3/Da / Density % sol: 49.54 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 1.5M Ammonium Sulfate, 100 mM Sodium Citrate pH5.5

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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: Oct 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97869 Å / Relative weight: 1
ReflectionResolution: 1.28→64.74 Å / Num. obs: 61963 / % possible obs: 90.6 % / Redundancy: 15 % / Biso Wilson estimate: 15.89 Å2 / CC1/2: 1 / Net I/σ(I): 33.6
Reflection shellResolution: 1.28→1.35 Å / Num. unique obs: 7996 / CC1/2: 0.898

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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: 1.34→30.06 Å / SU ML: 0.1326 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.5851
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1708 2023 3.43 %
Rwork0.1642 56937 -
obs0.1644 58960 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.57 Å2
Refinement stepCycle: LAST / Resolution: 1.34→30.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1788 0 27 271 2086
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00841848
X-RAY DIFFRACTIONf_angle_d1.20092498
X-RAY DIFFRACTIONf_chiral_restr0.0805287
X-RAY DIFFRACTIONf_plane_restr0.0102316
X-RAY DIFFRACTIONf_dihedral_angle_d11.4928255
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.34-1.380.26161410.22744030X-RAY DIFFRACTION99.98
1.38-1.410.25881420.21274032X-RAY DIFFRACTION100
1.41-1.460.21561400.19464042X-RAY DIFFRACTION100
1.46-1.50.18571430.18683994X-RAY DIFFRACTION99.98
1.5-1.560.1881460.17964053X-RAY DIFFRACTION100
1.56-1.620.20891450.17414011X-RAY DIFFRACTION100
1.62-1.690.19371380.17024034X-RAY DIFFRACTION100
1.69-1.780.18161480.16114056X-RAY DIFFRACTION100
1.78-1.890.18071440.16594033X-RAY DIFFRACTION100
1.89-2.040.13881460.15334079X-RAY DIFFRACTION100
2.04-2.240.15091470.15274065X-RAY DIFFRACTION100
2.25-2.570.13941440.14534107X-RAY DIFFRACTION100
2.57-3.240.16021470.16214128X-RAY DIFFRACTION100
3.24-30.060.17991520.16644273X-RAY DIFFRACTION99.91

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