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

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Basic information

Entry
Database: PDB / ID: 7twk
TitleStructure of a borosin methyltransferase from Mycena rosella with native peptide (MroMA1) in complex with SAH
Components(MroMA1) x 2
KeywordsTRANSFERASE / RIPPs / methyltransferase / borosin / MroMA
Function / homologyS-ADENOSYL-L-HOMOCYSTEINE
Function and homology information
Biological speciesMycena rosella (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MroMA1
B: MroMA1
C: MroMA1
D: MroMA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,61910
Polymers175,8974
Non-polymers1,7226
Water29,2561624
1
A: MroMA1
B: MroMA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,8095
Polymers87,9482
Non-polymers8613
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13550 Å2
ΔGint-82 kcal/mol
Surface area30530 Å2
MethodPISA
2
C: MroMA1
D: MroMA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,8095
Polymers87,9482
Non-polymers8613
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12400 Å2
ΔGint-75 kcal/mol
Surface area30250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)191.833, 191.833, 93.709
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein MroMA1


Mass: 43953.145 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycena rosella (fungus) / Production host: Escherichia coli (E. coli)
#2: Protein MroMA1


Mass: 43995.227 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycena rosella (fungus) / Production host: Escherichia coli (E. coli)
#3: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1624 / 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: 2.83 Å3/Da / Density % sol: 56.57 %
Crystal growTemperature: 282 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 5% PEG 3350, 200 mM ammonium acetate and 100 mM Tris-HCl buffer (pH=8.5)

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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: Nov 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.79→96 Å / Num. obs: 183361 / % possible obs: 100 % / Redundancy: 15.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.099 / Net I/σ(I): 21.2
Reflection shellResolution: 1.79→1.8 Å / Rmerge(I) obs: 1.326 / Mean I/σ(I) obs: 2 / Num. unique obs: 1837 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.24data extraction
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5N0S

5n0s


Resolution: 1.79→25 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.26 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN
RfactorNum. reflection% reflectionSelection details
Rfree0.192 9013 4.9 %RANDOM
Rwork0.167 ---
obs0.168 174260 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 mean: 30.62 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20.24 Å20 Å2
2--0.47 Å20 Å2
3----1.53 Å2
Refinement stepCycle: LAST / Resolution: 1.79→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11793 0 116 1624 13533
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01212321
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0531.64316747
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.73651546
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.05322.343606
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.894152033
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2251574
X-RAY DIFFRACTIONr_chiral_restr0.0840.21661
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029367
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.79→1.84 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 688 -
Rwork0.266 12752 -
obs--99.88 %

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