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- PDB-6tsc: OphMA I407P complex with SAH -

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Basic information

Entry
Database: PDB / ID: 6tsc
TitleOphMA I407P complex with SAH
Components
  • GLY-PHE-PRO-TRP-MVA-ILE-MVA-VAL-GLY-VAL-PRO-GLY
  • Peptide N-methyltransferase
KeywordsTRANSFERASE / Peptide bond N-methyltransferase
Function / homology
Function and homology information


Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / methylation
Similarity search - Function
Tetrapyrrole methylase / Tetrapyrrole (Corrin/Porphyrin) Methylases / Tetrapyrrole methylase, subdomain 1 / Tetrapyrrole methylase superfamily
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Peptide N-methyltransferase / Methyltransferase/ribosomally synthesized cyclic peptide omphalotin A precursor ophMA
Similarity search - Component
Biological speciesOmphalotus olearius (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsSong, H. / Naismith, J.H.
CitationJournal: Acs Chem.Biol. / Year: 2020
Title: Substrate Plasticity of a Fungal Peptide alpha-N-Methyltransferase.
Authors: Song, H. / Fahrig-Kamarauskaite, J.R. / Matabaro, E. / Kaspar, H. / Shirran, S.L. / Zach, C. / Pace, A. / Stefanov, B.A. / Naismith, J.H. / Kunzler, M.
History
DepositionDec 20, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptide N-methyltransferase
B: GLY-PHE-PRO-TRP-MVA-ILE-MVA-VAL-GLY-VAL-PRO-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2583
Polymers46,8732
Non-polymers3841
Water543
1
A: Peptide N-methyltransferase
B: GLY-PHE-PRO-TRP-MVA-ILE-MVA-VAL-GLY-VAL-PRO-GLY
hetero molecules

A: Peptide N-methyltransferase
B: GLY-PHE-PRO-TRP-MVA-ILE-MVA-VAL-GLY-VAL-PRO-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,5156
Polymers93,7474
Non-polymers7692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area16160 Å2
ΔGint-97 kcal/mol
Surface area28700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.379, 89.379, 157.001
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Peptide N-methyltransferase


Mass: 45618.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Omphalotus olearius (fungus) / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A2R2JFI5
#2: Protein/peptide GLY-PHE-PRO-TRP-MVA-ILE-MVA-VAL-GLY-VAL-PRO-GLY


Mass: 1254.519 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Omphalotus olearius (fungus) / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A2R2JFH9*PLUS
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 3.86 Å3/Da / Density % sol: 68.15 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.3-0.4 M KSCN, 0.1 M Bicine pH 8-9, 1.8-2.5 M sodium malonate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.19→52.33 Å / Num. obs: 38116 / % possible obs: 100 % / Redundancy: 11.1 % / CC1/2: 1 / Rrim(I) all: 0.058 / Net I/σ(I): 15.7
Reflection shellResolution: 2.19→2.23 Å / Redundancy: 10.9 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1877 / CC1/2: 0.9 / Rrim(I) all: 2.088 / % possible all: 99.7

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Processing

Software
NameVersionClassification
xia2data scaling
REFMAC5.8.0257refinement
PDB_EXTRACT3.25data extraction
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5N0O

5n0o


Resolution: 2.19→52.33 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.96 / SU B: 23.313 / SU ML: 0.218 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.163 / ESU R Free: 0.149
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2322 1846 4.9 %RANDOM
Rwork0.2078 ---
obs0.209 36209 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å
Displacement parametersBiso max: 192.48 Å2 / Biso mean: 99.841 Å2 / Biso min: 60.55 Å2
Baniso -1Baniso -2Baniso -3
1-2.87 Å21.44 Å20 Å2
2--2.87 Å20 Å2
3----9.31 Å2
Refinement stepCycle: final / Resolution: 2.19→52.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2960 0 26 3 2989
Biso mean--73.97 67.68 -
Num. residues----381
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0133058
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172831
X-RAY DIFFRACTIONr_angle_refined_deg1.5181.6484162
X-RAY DIFFRACTIONr_angle_other_deg1.1921.5736569
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9395376
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.78922.065155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.70915485
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3551520
X-RAY DIFFRACTIONr_chiral_restr0.0630.2398
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023426
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02625
LS refinement shellResolution: 2.19→2.247 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.436 114 -
Rwork0.453 2651 -
all-2765 -
obs--99.64 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.018-0.31830.48771.0531-0.19086.96790.2257-0.1797-0.0789-0.3552-0.19610.01950.4332-0.1722-0.02960.16410.0672-0.01140.18880.00480.205721.709236.1848-1.6541
211.7916-13.6131-7.459515.72678.57634.89840.11160.3727-0.747-0.1444-0.35510.91910.234-0.39240.24350.6777-0.0449-0.33640.46420.17380.507816.488633.6559-18.5669
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 401
2X-RAY DIFFRACTION2B397 - 408

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