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- PDB-7twm: Structure of a borosin methyltransferase from Mycena rosella with... -

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Basic information

Entry
Database: PDB / ID: 7twm
TitleStructure of a borosin methyltransferase from Mycena rosella with peptide CspL(MroMCspL) in complex with SAH
ComponentsMroMCspL
KeywordsTRANSFERASE / RIPPs / methyltransferase / borosin / MroMA
Function / homologyS-ADENOSYL-L-HOMOCYSTEINE
Function and homology information
Biological speciesMycena rosella (pink bonnet)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsZheng, Y. / Ongpipattanakul, C. / Nair, S.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM079038 United States
CitationJournal: Acs Catalysis / Year: 2022
Title: Bioconjugate Platform for Iterative Backbone N -Methylation of Peptides.
Authors: Zheng, Y. / Ongpipattanakul, C. / Nair, S.K.
History
DepositionFeb 7, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.mon_nstd_flag / _chem_comp.type / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MroMCspL
B: MroMCspL
C: MroMCspL
D: MroMCspL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,5238
Polymers175,9854
Non-polymers1,5384
Water15,439857
1
A: MroMCspL
B: MroMCspL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,7614
Polymers87,9932
Non-polymers7692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13070 Å2
ΔGint-86 kcal/mol
Surface area30680 Å2
MethodPISA
2
C: MroMCspL
D: MroMCspL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,7614
Polymers87,9932
Non-polymers7692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12040 Å2
ΔGint-77 kcal/mol
Surface area30230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)190.960, 190.960, 93.589
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein
MroMCspL


Mass: 43996.301 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycena rosella (pink bonnet) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 857 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.82 Å3/Da / Density % sol: 56.33 %
Crystal growTemperature: 282 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 25% PEG 4000, and 100 mM sodium cacodylate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.93→82.7 Å / Num. obs: 145206 / % possible obs: 99.5 % / Redundancy: 13.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.109 / Net I/σ(I): 18.9
Reflection shellResolution: 1.93→1.94 Å / Rmerge(I) obs: 1.31 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1457 / % possible all: 94

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.24data extraction
autoPROC1.0.5data reduction
autoPROC1.0.5data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7TWK

7twk


Resolution: 1.93→25 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.071 / SU ML: 0.087 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.131 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2019 7166 4.9 %RANDOM
Rwork0.1739 ---
obs0.1753 137966 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 154.99 Å2 / Biso mean: 34.743 Å2 / Biso min: 15.53 Å2
Baniso -1Baniso -2Baniso -3
1-0.55 Å20.27 Å2-0 Å2
2--0.55 Å20 Å2
3----1.77 Å2
Refinement stepCycle: final / Resolution: 1.93→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11725 0 104 857 12686
Biso mean--22.85 38.55 -
Num. residues----1520
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01212123
X-RAY DIFFRACTIONr_angle_refined_deg1.1411.6416464
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.87351516
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.14722.203590
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.564151997
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8481574
X-RAY DIFFRACTIONr_chiral_restr0.0880.21625
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029200
LS refinement shellResolution: 1.932→1.982 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 477 -
Rwork0.251 10133 -
all-10610 -
obs--99.87 %

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