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- PDB-7v6l: LcCOMT in complex with SAH -

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Basic information

Entry
Database: PDB / ID: 7v6l
TitleLcCOMT in complex with SAH
ComponentsLcCOMT
KeywordsTRANSFERASE / SAM / complex
Function / homologyS-ADENOSYL-L-HOMOCYSTEINE
Function and homology information
Biological speciesLigusticum chuanxiong (chuang-xiong)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.948 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)80,6774
Polymers79,9082
Non-polymers7692
Water5,927329
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8540 Å2
ΔGint-75 kcal/mol
Surface area26480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.393, 60.169, 129.901
Angle α, β, γ (deg.)90.000, 95.260, 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-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 329 / 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: 2.26 Å3/Da / Density % sol: 45.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M Ammonium acetate, 0.1 M BIS-TRIS pH 6.5, 25% w/v Polyethylene glycol 3350

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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: 1.948→50 Å / Num. obs: 51456 / % possible obs: 98.7 % / Redundancy: 6.6 % / Rrim(I) all: 0.129 / Net I/σ(I): 14
Reflection shellResolution: 1.948→2 Å / Num. unique obs: 3108 / CC1/2: 0.939

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3reo

3reo


Resolution: 1.948→44.053 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2337 2193 4.96 %
Rwork0.1923 41980 -
obs0.1943 44173 84.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.42 Å2 / Biso mean: 27.3956 Å2 / Biso min: 2.9 Å2
Refinement stepCycle: final / Resolution: 1.948→44.053 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5332 0 90 329 5751
Biso mean--20.62 24.64 -
Num. residues----691
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9481-1.99050.2428660.2257154350
1.9905-2.03680.2931060.2341181759
2.0368-2.08770.2851050.2246195163
2.0877-2.14420.27561120.2141209168
2.1442-2.20730.26351280.2123220271
2.2073-2.27850.25231250.2078236777
2.2785-2.35990.23961400.2198255283
2.3599-2.45440.24251440.2115272087
2.4544-2.56610.25321520.2099289994
2.5661-2.70140.24491550.2159306999
2.7014-2.87060.2671660.20293080100
2.8706-3.09220.23661670.20633101100
3.0922-3.40330.24881650.19093097100
3.4033-3.89550.21141550.17653126100
3.8955-4.90680.18181440.15133150100
4.9068-44.0530.20741630.17463215100

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