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- PDB-5n0t: Crystal structure of OphA-DeltaC6 mutant Y76F in complex with SAM -

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Basic information

Entry
Database: PDB / ID: 5n0t
TitleCrystal structure of OphA-DeltaC6 mutant Y76F in complex with SAM
ComponentsPeptide N-methyltransferase
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-ADENOSYLMETHIONINE / Methyltransferase/ribosomally synthesized cyclic peptide omphalotin A precursor ophMA
Function and homology information
Biological speciesOmphalotus olearius (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)90,7974
Polymers90,0002
Non-polymers7972
Water10,953608
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14790 Å2
ΔGint-90 kcal/mol
Surface area31070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.081, 93.541, 86.643
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-899-

HOH

21B-891-

HOH

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Components

#1: Protein Peptide N-methyltransferase


Mass: 45000.137 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: A0A2R2JFI1*PLUS
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 608 / Source method: isolated from a natural source / Formula: H2O
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

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: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9281 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9281 Å / Relative weight: 1
ReflectionResolution: 1.78→83 Å / Num. obs: 129666 / % possible obs: 100 % / Redundancy: 7.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Net I/σ(I): 1.2
Reflection shellResolution: 1.78→1.81 Å / Redundancy: 7.2 % / Rmerge(I) obs: 1.622 / Mean I/σ(I) obs: 1.2 / CC1/2: 0.565 / % possible all: 98.6

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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: 1.78→83 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.954 / SU B: 6.472 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.101 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23229 6242 4.9 %RANDOM
Rwork0.2107 ---
obs0.21177 121216 98.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 37.426 Å2
Baniso -1Baniso -2Baniso -3
1-2.73 Å20 Å20 Å2
2---2.1 Å20 Å2
3----0.63 Å2
Refinement stepCycle: 1 / Resolution: 1.78→83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6104 0 54 608 6766
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0196423
X-RAY DIFFRACTIONr_bond_other_d0.0010.025957
X-RAY DIFFRACTIONr_angle_refined_deg1.4291.9778758
X-RAY DIFFRACTIONr_angle_other_deg0.956313844
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9245814
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.27323.893280
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.693151033
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2421542
X-RAY DIFFRACTIONr_chiral_restr0.0890.2976
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217187
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021285
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_it12.1573211
X-RAY DIFFRACTIONr_mcbond_other12.1573211
X-RAY DIFFRACTIONr_mcangle_it1.8193.2154019
X-RAY DIFFRACTIONr_mcangle_other1.8193.2154020
X-RAY DIFFRACTIONr_scbond_it0.8422.2253212
X-RAY DIFFRACTIONr_scbond_other0.8422.2243213
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.5143.3084733
X-RAY DIFFRACTIONr_long_range_B_refined5.77726.6286954
X-RAY DIFFRACTIONr_long_range_B_other5.59725.4676776
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.78→1.826 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 442 -
Rwork0.414 8607 -
obs--95.45 %
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)
10.44510.0757-0.01941.99910.23940.59040.0209-0.01550.01270.03630.05430.15150.02620.0342-0.07530.00460.00720.00810.1349-0.02290.083927.757946.908121.6925
20.4365-0.0244-0.16151.9550.23660.56190.0065-0.00810.0258-0.03650.06330.1299-0.00720.0446-0.06980.0012-0.00750.00190.136-0.01910.081327.761347.71621.3007
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 501
2X-RAY DIFFRACTION2B7 - 501

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