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- PDB-5n0q: Crystal structure of OphA-DeltaC6 in complex with SAH -

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Basic information

Entry
Database: PDB / ID: 5n0q
TitleCrystal structure of OphA-DeltaC6 in complex with SAH
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-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: 2.402 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.mon_nstd_flag / _chem_comp.type

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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)90,9374
Polymers90,1692
Non-polymers7692
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13470 Å2
ΔGint-80 kcal/mol
Surface area30100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.443, 102.424, 115.297
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-methyltransferase


Mass: 45084.301 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: A0A2R2JFI5*PLUS
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.25 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.02 % octyl beta-D-glucopyranoside (OG), 0.2 M KCl, 0.1 M Bis-Tris pH 6.5 and 20% PEG 4000

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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: 2.4→61.34 Å / Num. obs: 33901 / % possible obs: 99.2 % / Redundancy: 4.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.074 / Net I/σ(I): 11.9
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 4.4 % / Rmerge(I) obs: 1.009 / Mean I/σ(I) obs: 2.2 / CC1/2: 0.861 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5N0O

5n0o


Resolution: 2.402→61.34 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.94
RfactorNum. reflection% reflection
Rfree0.2688 1619 4.79 %
Rwork0.2226 --
obs0.2248 33795 98.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.402→61.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5832 0 52 15 5899
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076021
X-RAY DIFFRACTIONf_angle_d1.2738193
X-RAY DIFFRACTIONf_dihedral_angle_d12.3383655
X-RAY DIFFRACTIONf_chiral_restr0.08911
X-RAY DIFFRACTIONf_plane_restr0.0071076
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4017-2.47240.44311370.38492609X-RAY DIFFRACTION99
2.4724-2.55220.46011470.36072623X-RAY DIFFRACTION99
2.5522-2.64340.34031210.33742672X-RAY DIFFRACTION99
2.6434-2.74920.42421170.31652664X-RAY DIFFRACTION99
2.7492-2.87440.34581350.30112657X-RAY DIFFRACTION99
2.8744-3.02590.30541250.26542697X-RAY DIFFRACTION99
3.0259-3.21550.31461280.26342658X-RAY DIFFRACTION99
3.2155-3.46370.29371110.24972716X-RAY DIFFRACTION100
3.4637-3.81230.27141530.2282664X-RAY DIFFRACTION99
3.8123-4.36380.24051620.18922672X-RAY DIFFRACTION99
4.3638-5.49730.21191340.17492739X-RAY DIFFRACTION99
5.4973-61.35990.22761490.17882805X-RAY DIFFRACTION97
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)
12.94571.6080.55614.3221-0.07572.5850.1989-0.3792-0.02420.5073-0.2624-0.62010.18150.11860.03020.4711-0.052-0.0970.4789-0.00150.4836-2.56447.8313-17.6802
21.9556-0.31230.0750.8461-0.31080.0519-0.2772-0.11531.43570.54150.00080.4784-0.1792-0.17540.11870.82530.1803-0.17910.7078-0.27341.4218-26.964834.2138-20.6165
32.88690.35551.27642.26461.32073.470.12440.1370.2108-0.3596-0.00060.9388-0.1164-0.537-0.14320.6532-0.1561-0.03280.60010.06181.0258-31.09393.3993-33.4214
42.3635-0.22760.19393.2483-0.79312.86040.3554-0.26720.191-0.0256-0.08661.41590.2997-0.8207-0.2690.5649-0.161-0.01080.7145-0.03851.0346-30.58861.8358-22.7744
52.5348-0.08860.26620.97610.27162.80750.1525-1.01540.70140.4608-0.20111.9697-0.0869-0.7963-0.02110.579-0.10020.29040.9037-0.1811.2349-31.087710.208-14.6597
62.98220.96970.17054.3265-0.32431.5854-0.23490.1880.8532-0.91730.08391.1996-0.1627-0.1920.1710.635-0.0466-0.22050.47650.03270.7851-16.323721.8482-34.0981
70.845-0.1648-1.03184.0057-0.95551.7511-0.06130.28290.3732-0.4475-0.0831-0.4877-0.14680.58050.14840.6693-0.1318-0.02910.48860.04660.6297-2.111822.1492-31.4926
82.91190.22050.19963.9801-0.50482.88990.1066-0.6616-0.82360.3971-0.2813-0.88760.7640.38480.11030.6818-0.0733-0.09230.60290.18930.9726-2.371-6.6616-13.0151
93.0031-0.16280.49744.7108-0.58533.0917-0.0937-0.7838-0.84790.9070.3475-0.9661.0703-0.1942-0.4031.1826-0.1311-0.30070.74730.21591.1641-1.7261-6.8531-2.8808
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 248 )
2X-RAY DIFFRACTION2chain 'A' and (resid 249 through 283 )
3X-RAY DIFFRACTION3chain 'A' and (resid 284 through 411 )
4X-RAY DIFFRACTION4chain 'B' and (resid 8 through 71 )
5X-RAY DIFFRACTION5chain 'B' and (resid 72 through 129 )
6X-RAY DIFFRACTION6chain 'B' and (resid 130 through 233 )
7X-RAY DIFFRACTION7chain 'B' and (resid 234 through 289 )
8X-RAY DIFFRACTION8chain 'B' and (resid 290 through 356 )
9X-RAY DIFFRACTION9chain 'B' and (resid 357 through 411 )

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