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- PDB-7v6j: LcCOMT in complex with SAM -

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Basic information

Entry
Database: PDB / ID: 7v6j
TitleLcCOMT in complex with SAM
ComponentsLcCOMT
KeywordsTRANSFERASE / SAM / complex
Function / homologyS-ADENOSYLMETHIONINE
Function and homology information
Biological speciesLigusticum chuanxiong (chuang-xiong)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.799 Å
AuthorsYu, Y. / CHen, Q.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Int.J.Biol.Macromol. / Year: 2022
Title: Structure basis of the caffeic acid O-methyltransferase from Ligusiticum chuanxiong to understand its selective mechanism.
Authors: Song, S. / Chen, A. / Zhu, J. / Yan, Z. / An, Q. / Zhou, J. / Liao, H. / Yu, Y.
History
DepositionAug 20, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 29, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LcCOMT
B: LcCOMT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,7285
Polymers79,9082
Non-polymers8203
Water12,647702
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8800 Å2
ΔGint-86 kcal/mol
Surface area27480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.960, 60.124, 132.192
Angle α, β, γ (deg.)90.000, 96.070, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein LcCOMT


Mass: 39954.176 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ligusticum chuanxiong (chuang-xiong) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 702 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M Sodium chloride, 0.1 M BIS-TRIS pH 6.5, 25% Polyethylene glycol 3350, 20% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97774 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97774 Å / Relative weight: 1
ReflectionResolution: 1.799→50 Å / Num. obs: 68127 / % possible obs: 99.9 % / Redundancy: 6.8 % / Rrim(I) all: 0.134 / Net I/σ(I): 16
Reflection shellResolution: 1.799→1.84 Å / Num. unique obs: 4475 / CC1/2: 0.896

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3REO

3reo


Resolution: 1.799→46.697 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2112 1330 2.01 %
Rwork0.1705 64870 -
obs0.1713 66200 96.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.52 Å2 / Biso mean: 26.4419 Å2 / Biso min: 6.29 Å2
Refinement stepCycle: final / Resolution: 1.799→46.697 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5304 0 97 702 6103
Biso mean--24.47 32.38 -
Num. residues----687
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.799-1.86330.29121050.2167550483
1.8633-1.93790.24471370.2006605792
1.9379-2.02610.25261330.1976652898
2.0261-2.13290.24841460.181659199
2.1329-2.26660.22931530.17416611100
2.2666-2.44150.20691290.15896635100
2.4415-2.68720.21481340.16966669100
2.6872-3.0760.21431550.16966684100
3.076-3.87520.1917980.16056762100
3.8752-46.6970.17731400.1616829100

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