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- PDB-5n0w: Crystal structure of OphA-DeltaC6 mutant R72A in complex with SAM -

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Basic information

Entry
Database: PDB / ID: 5n0w
TitleCrystal structure of OphA-DeltaC6 mutant R72A 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 / MOLECULAR REPLACEMENT / Resolution: 1.93 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)90,7175
Polymers89,8282
Non-polymers8893
Water9,620534
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14920 Å2
ΔGint-87 kcal/mol
Surface area30110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.098, 92.276, 85.684
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
11B-851-

HOH

21B-857-

HOH

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Components

#1: Protein Peptide N-methyltransferase


Mass: 44914.023 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: A0A2R2JFI2*PLUS
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 534 / 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: 3.59 Å3/Da / Density % sol: 65.73 %
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 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.93→49.8 Å / Num. obs: 96972 / % possible obs: 98.7 % / Redundancy: 4.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.071 / Net I/σ(I): 17.4
Reflection shellResolution: 1.93→2.02 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.568 / Mean I/σ(I) obs: 1.3 / CC1/2: 0.768 / % possible all: 97.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5N0O

5n0o


Resolution: 1.93→49.8 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.951 / SU B: 6.827 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21609 4911 5.1 %RANDOM
Rwork0.19363 ---
obs0.19476 91990 98.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.126 Å2
Baniso -1Baniso -2Baniso -3
1-1.51 Å20 Å20 Å2
2---0.48 Å20 Å2
3----1.02 Å2
Refinement stepCycle: 1 / Resolution: 1.93→49.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6071 0 60 534 6665
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0196325
X-RAY DIFFRACTIONr_bond_other_d0.0020.025830
X-RAY DIFFRACTIONr_angle_refined_deg1.381.9778616
X-RAY DIFFRACTIONr_angle_other_deg0.922313552
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7825790
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.52724.265279
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.486151011
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8941537
X-RAY DIFFRACTIONr_chiral_restr0.080.2960
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217051
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021240
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_it1.243.3253163
X-RAY DIFFRACTIONr_mcbond_other1.243.3253163
X-RAY DIFFRACTIONr_mcangle_it2.1674.9713952
X-RAY DIFFRACTIONr_mcangle_other2.1664.973953
X-RAY DIFFRACTIONr_scbond_it1.2313.4853162
X-RAY DIFFRACTIONr_scbond_other1.2313.4853162
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.125.174665
X-RAY DIFFRACTIONr_long_range_B_refined5.81440.237131
X-RAY DIFFRACTIONr_long_range_B_other5.58339.3456969
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.927→1.977 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 359 -
Rwork0.302 6521 -
obs--95.93 %
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)
10.580.15010.01041.4935-0.19740.5553-0.038-0.0015-0.0086-0.0090.0855-0.1885-0.02930.0007-0.04750.04840.0002-0.0040.01570.00060.0533135.708-0.3268150.0786
20.5461-0.02520.09981.4363-0.21640.5135-0.0402-0.0077-0.0353-0.11120.0879-0.18630.0226-0.0157-0.04760.0524-0.0074-0.00130.0140.00110.0595135.6205-1.3629149.4589
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 501
2X-RAY DIFFRACTION2B7 - 502

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