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- PDB-6qzy: full length OphA V406P in complex with SAH -

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Basic information

Entry
Database: PDB / ID: 6qzy
Titlefull length OphA V406P in complex with SAH
Components
  • ASN-GLY-PHE-PRO-TRP-MVA-ILE-MVA-VAL-GLY-PRO-ILE-GLY
  • Peptide N-methyltransferase
KeywordsTRANSFERASE / Peptide bond N-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
S-ADENOSYL-L-HOMOCYSTEINE / THIOCYANATE ION / Methyltransferase/ribosomally synthesized cyclic peptide omphalotin A precursor ophMA / Methyltransferase/ribosomally synthesized cyclic peptide omphalotin A precursor ophMA
Similarity search - Component
Biological speciesOmphalotus olearius (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsSong, H. / Naismith, J.H.
CitationJournal: Acs Chem.Biol. / Year: 2020
Title: Substrate Plasticity of a Fungal Peptide alpha-N-Methyltransferase.
Authors: Song, H. / Fahrig-Kamarauskaite, J.R. / Matabaro, E. / Kaspar, H. / Shirran, S.L. / Zach, C. / Pace, A. / Stefanov, B.A. / Naismith, J.H. / Kunzler, M.
History
DepositionMar 12, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2020Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 29, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / struct_conn / struct_conn_type
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.3Jan 24, 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: ASN-GLY-PHE-PRO-TRP-MVA-ILE-MVA-VAL-GLY-PRO-ILE-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3865
Polymers47,9202
Non-polymers4673
Water3,153175
1
A: Peptide N-methyltransferase
B: ASN-GLY-PHE-PRO-TRP-MVA-ILE-MVA-VAL-GLY-PRO-ILE-GLY
hetero molecules

A: Peptide N-methyltransferase
B: ASN-GLY-PHE-PRO-TRP-MVA-ILE-MVA-VAL-GLY-PRO-ILE-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,77310
Polymers95,8394
Non-polymers9346
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area16970 Å2
ΔGint-108 kcal/mol
Surface area30250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.047, 92.447, 162.763
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-653-

HOH

21A-699-

HOH

31A-767-

HOH

41A-771-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Peptide N-methyltransferase


Mass: 45632.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Omphalotus olearius (fungus) / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A2R2JFI5*PLUS
#2: Protein/peptide ASN-GLY-PHE-PRO-TRP-MVA-ILE-MVA-VAL-GLY-PRO-ILE-GLY


Mass: 2286.689 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Omphalotus olearius (fungus) / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A2R2JFH4*PLUS

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Non-polymers , 4 types, 178 molecules

#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Chemical ChemComp-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 3.38 Å3/Da / Density % sol: 63.58 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.3-0.4 M KSCN, 0.1 M bicine pH 9, 1.8-2.2 M sodium malonate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.61→80.39 Å / Num. all: 599482 / Num. obs: 84065 / % possible obs: 100 % / Redundancy: 7.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Net I/σ(I): 13.6
Reflection shellResolution: 1.61→1.65 Å / Redundancy: 7.2 % / Rmerge(I) obs: 1.078 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 6118 / CC1/2: 0.776 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5N0O

5n0o


Resolution: 1.61→80.39 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.961 / SU B: 3.342 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.07 / ESU R Free: 0.069 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20489 4223 5 %RANDOM
Rwork0.19005 ---
obs0.19079 79829 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 39.096 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20 Å2
2---1.13 Å20 Å2
3---1.04 Å2
Refinement stepCycle: 1 / Resolution: 1.61→80.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3063 0 30 175 3268
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0133291
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173045
X-RAY DIFFRACTIONr_angle_refined_deg1.3111.6494486
X-RAY DIFFRACTIONr_angle_other_deg1.2911.5747080
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0115413
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.622.061165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.34615528
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9121522
X-RAY DIFFRACTIONr_chiral_restr0.0630.2429
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023724
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02669
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_it1.1472.7531652
X-RAY DIFFRACTIONr_mcbond_other1.1482.751650
X-RAY DIFFRACTIONr_mcangle_it1.9784.1182069
X-RAY DIFFRACTIONr_mcangle_other1.9794.1182069
X-RAY DIFFRACTIONr_scbond_it1.3432.9241638
X-RAY DIFFRACTIONr_scbond_other1.3422.9251639
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1874.3182418
X-RAY DIFFRACTIONr_long_range_B_refined4.30731.6713455
X-RAY DIFFRACTIONr_long_range_B_other4.30731.6693455
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.609→1.651 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 335 -
Rwork0.272 5675 -
obs--97.61 %
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)
10.5015-0.26720.00591.3365-0.11020.5721-0.03680.01730.0245-0.16920.0911-0.0560.00230.0088-0.05440.0529-0.00730.00350.0165-0.00240.01830.25371.063927.6355
24.6428-0.6504-3.36280.68210.48873.7151-0.01050.20410.1485-0.28890.00740.0287-0.1932-0.24760.00310.1716-0.0021-0.03970.0290.01580.0481-6.895417.093424.2819
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 602
2X-RAY DIFFRACTION2B396 - 408

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