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- PDB-7wzf: Structural and mechanism analysis of YunM -

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Basic information

Entry
Database: PDB / ID: 7wzf
TitleStructural and mechanism analysis of YunM
ComponentsYunM
KeywordsTRANSFERASE / Linaridin Methyltransferase
Function / homologyS-ADENOSYL-L-HOMOCYSTEINE
Function and homology information
Biological speciesStreptomyces yunnanensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsDuan, S.Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structural and mechanism analysis of YunM
Authors: Duan, S.Y.
History
DepositionFeb 18, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 22, 2023Provider: 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: YunM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1912
Polymers29,8061
Non-polymers3841
Water4,017223
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, monomer in solution
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.741, 107.741, 109.163
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein YunM


Mass: 29806.436 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The sequence has been deposited to NCBI with accession code WP_073444433.1, and contains tag sequence MGSSHHHHHHSSGLVPRGSH at N-terminal.
Source: (gene. exp.) Streptomyces yunnanensis (bacteria) / 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.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 3.31 Å3/Da / Density % sol: 62.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: Under the condition of 2000 mM ammonium sulfate, 100 mM CAPS/ sodium hydroxide pH 10.5, 200 mM lithium sulfate an initial crystallization condition was identified over 3 weeks and was ...Details: Under the condition of 2000 mM ammonium sulfate, 100 mM CAPS/ sodium hydroxide pH 10.5, 200 mM lithium sulfate an initial crystallization condition was identified over 3 weeks and was subsequently optimized to yield well-diffracting crystals. Final optimized conditions for YunM with SAM contained 1800 mM ammonium sulfate, 100 mM CAPS/sodium hydroxide pH 10.4, 100 mM lithium sulfate, and yielded square crystals

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 73359 / % possible obs: 99.7 % / Redundancy: 1.1 % / CC1/2: 0.992 / Net I/σ(I): 37.4
Reflection shellResolution: 1.4→1.42 Å / Num. unique obs: 7005 / CC1/2: 0.836

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HH4

4hh4


Resolution: 1.4→23.33 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2178 3763 5.13 %
Rwork0.2058 69593 -
obs0.2064 73356 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 45.89 Å2 / Biso mean: 17.5102 Å2 / Biso min: 8.4 Å2
Refinement stepCycle: final / Resolution: 1.4→23.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1874 0 26 227 2127
Biso mean--13.04 25.34 -
Num. residues----243
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.420.31251430.30172367251093
1.42-1.440.30371300.27262498262898
1.44-1.460.25971290.242825542683100
1.46-1.480.24591560.223925162672100
1.48-1.50.2371330.224625422675100
1.5-1.520.22621510.21225402691100
1.52-1.550.21511300.201125602690100
1.55-1.570.23111400.20525302670100
1.57-1.60.20961290.198725872716100
1.6-1.630.21581200.208725812701100
1.63-1.670.23011520.209425472699100
1.67-1.70.19951460.212425512697100
1.7-1.740.25031340.209325682702100
1.74-1.790.22071100.209825882698100
1.79-1.830.22681280.20125602688100
1.83-1.890.21761420.203725852727100
1.89-1.950.21271450.196825602705100
1.95-2.020.22181460.199125782724100
2.02-2.10.19041430.201125912734100
2.1-2.20.20541520.198625692721100
2.2-2.310.20871490.196725792728100
2.31-2.460.23251340.199326232757100
2.46-2.650.21381410.216626112752100
2.65-2.910.2111220.210626512773100
2.91-3.330.20991450.210526512796100
3.33-4.190.20991570.194226782835100
4.19-23.330.21881560.20032828298499

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