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- PDB-5n0s: Crystal structure of OphA-DeltaC6 mutant Y98A in complex with SAM -

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Basic information

Entry
Database: PDB / ID: 5n0s
TitleCrystal structure of OphA-DeltaC6 mutant Y98A in complex with SAM
ComponentsPeptide N-methyltransferase
KeywordsTRANSFERASE / 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
MALONATE ION / S-ADENOSYLMETHIONINE / Methyltransferase/ribosomally synthesized cyclic peptide omphalotin A precursor ophMA
Similarity search - Component
Biological speciesOmphalotus olearius (fungus)
MethodX-RAY DIFFRACTION / Resolution: 1.95 Å
AuthorsSong, H. / Naismith, J.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptide N-methyltransferase
B: Peptide N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,8176
Polymers89,8162
Non-polymers1,0014
Water9,440524
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15730 Å2
ΔGint-81 kcal/mol
Surface area30900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.906, 92.521, 85.332
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Peptide N-methyltransferase


Mass: 44908.043 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: A0A2R2JFI0*PLUS
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 524 / Source method: isolated from a natural source / Formula: H2O

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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: 3.6 Å3/Da / Density % sol: 65.85 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.3-0.4 M KSCN, 1.5-1.9 M sodium malonate and 0.1 M bicine pH 9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Oct 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.95→85.33 Å / Num. obs: 93739 / % possible obs: 98.4 % / Redundancy: 5.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.098 / Net I/σ(I): 6.7
Reflection shellResolution: 1.95→2.09 Å / Redundancy: 4.5 % / Rmerge(I) obs: 1.017 / Mean I/σ(I) obs: 1 / CC1/2: 0.657 / % possible all: 95.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
Aimlessdata scaling
PHASERphasing
RefinementStarting model: 5N0o

5n0o


Resolution: 1.95→85.33 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.954 / SU B: 7.475 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23335 4632 4.9 %RANDOM
Rwork0.20526 ---
obs0.20663 88960 98.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.812 Å2
Baniso -1Baniso -2Baniso -3
1-1.7 Å20 Å20 Å2
2---0.67 Å20 Å2
3----1.03 Å2
Refinement stepCycle: 1 / Resolution: 1.95→85.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6215 0 68 524 6807
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0196526
X-RAY DIFFRACTIONr_bond_other_d0.0020.026016
X-RAY DIFFRACTIONr_angle_refined_deg1.4391.9758884
X-RAY DIFFRACTIONr_angle_other_deg0.938313992
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0795819
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.36124.236288
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.948151050
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8931540
X-RAY DIFFRACTIONr_chiral_restr0.0810.2987
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217287
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021275
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_it1.3673.373267
X-RAY DIFFRACTIONr_mcbond_other1.3673.373267
X-RAY DIFFRACTIONr_mcangle_it2.3765.0464083
X-RAY DIFFRACTIONr_mcangle_other2.3765.0464084
X-RAY DIFFRACTIONr_scbond_it1.2993.4713259
X-RAY DIFFRACTIONr_scbond_other1.2963.4693257
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1975.1414799
X-RAY DIFFRACTIONr_long_range_B_refined5.54240.9057326
X-RAY DIFFRACTIONr_long_range_B_other5.54340.887324
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 330 -
Rwork0.316 5930 -
obs--89.77 %
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)
10.4501-0.0313-0.11361.51330.15450.5597-0.0215-0.00670.0145-0.06830.0770.149-0.00170.0352-0.05550.0111-0.00330.0040.0357-0.00270.054191.377492.8145105.9212
20.46580.06490.04861.69010.20240.6241-0.0242-0.02080.02040.03580.08580.1602-0.01740.024-0.06160.00790.00660.01280.0316-0.00240.0459191.311393.0082107.1697
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 501
2X-RAY DIFFRACTION2B7 - 501

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