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- PDB-5n0p: Crystal structure of OphA-DeltaC18 in complex with SAH -

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Basic information

Entry
Database: PDB / ID: 5n0p
TitleCrystal structure of OphA-DeltaC18 in complex with SAH
Componentspeptide N-methyltranferase
KeywordsTRANSFERASE / methyltransferase
Function / homologyTetrapyrrole methylase / Tetrapyrrole (Corrin/Porphyrin) Methylases / Tetrapyrrole methylase, subdomain 1 / Tetrapyrrole methylase superfamily / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / methylation / S-ADENOSYL-L-HOMOCYSTEINE / Methyltransferase/ribosomally synthesized cyclic peptide omphalotin A precursor ophMA
Function and homology information
Biological speciesOmphalotus olearius (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsNaismith, J.H. / Song, H.
CitationJournal: Sci Adv / Year: 2018
Title: A molecular mechanism for the enzymatic methylation of nitrogen atoms within peptide bonds.
Authors: Song, H. / van der Velden, N.S. / Shiran, S.L. / Bleiziffer, P. / Zach, C. / Sieber, R. / Imani, A.S. / Krausbeck, F. / Aebi, M. / Freeman, M.F. / Riniker, S. / Kunzler, M. / Naismith, J.H.
History
DepositionFeb 3, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 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
Revision 1.3Dec 10, 2025Group: Data collection / Structure summary / Category: chem_comp / pdbx_entry_details / Item: _chem_comp.mon_nstd_flag / _chem_comp.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: peptide N-methyltranferase
B: peptide N-methyltranferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,5086
Polymers87,6152
Non-polymers8934
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11820 Å2
ΔGint-55 kcal/mol
Surface area31430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.802, 100.216, 124.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein peptide N-methyltranferase


Mass: 43807.652 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Omphalotus olearius (fungus) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2R2JFH7*PLUS
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.79 Å3/Da / Density % sol: 55.84 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.04 M ammonium citrate tribasic, 0.1 M sodium citrate pH 5.5 and 27% PEG MME 5000.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9281 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9281 Å / Relative weight: 1
ReflectionResolution: 2.157→100.2 Å / Num. obs: 51104 / % possible obs: 99.9 % / Redundancy: 5.5 % / CC1/2: 1 / Rmerge(I) obs: 0.033 / Net I/σ(I): 20.9
Reflection shellResolution: 2.157→2.164 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.661 / CC1/2: 0.79 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5N0O

5n0o


Resolution: 2.16→78.06 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.953 / SU B: 11.919 / SU ML: 0.148 / Cross valid method: FREE R-VALUE / ESU R: 0.214 / ESU R Free: 0.173 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22628 2499 4.9 %RANDOM
Rwork0.20007 ---
obs0.20142 48538 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 72.243 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å20 Å2
2---0.66 Å20 Å2
3---0.54 Å2
Refinement stepCycle: 1 / Resolution: 2.16→78.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5728 0 60 120 5908
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195938
X-RAY DIFFRACTIONr_bond_other_d0.0010.025463
X-RAY DIFFRACTIONr_angle_refined_deg1.3151.9778073
X-RAY DIFFRACTIONr_angle_other_deg0.933312689
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6595735
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.59324.023266
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.26615951
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9331538
X-RAY DIFFRACTIONr_chiral_restr0.0760.2895
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216591
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021171
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_it1.334.0962955
X-RAY DIFFRACTIONr_mcbond_other1.334.0972954
X-RAY DIFFRACTIONr_mcangle_it2.3216.1313685
X-RAY DIFFRACTIONr_mcangle_other2.3216.1313686
X-RAY DIFFRACTIONr_scbond_it1.2794.2822983
X-RAY DIFFRACTIONr_scbond_other1.2784.2822983
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1766.3494389
X-RAY DIFFRACTIONr_long_range_B_refined4.5547.3796161
X-RAY DIFFRACTIONr_long_range_B_other4.55547.2866145
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.157→2.213 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 184 -
Rwork0.296 3551 -
obs--100 %
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)
13.04330.46840.12891.68810.1381.85950.1073-0.284-0.37030.1297-0.09150.10690.1901-0.3402-0.01580.0373-0.0751-0.03560.19450.14970.188613.532-14.0129-24.0016
22.66580.3241-0.20881.42830.3631.4971-0.0549-0.175-0.35350.1204-0.02940.01290.0872-0.17820.08430.0277-0.0409-0.02920.1550.12970.194317.2461-14.7938-24.5708
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 501
2X-RAY DIFFRACTION2B8 - 501

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