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- PDB-5n0n: Crystal structure of OphA-DeltaC6 mutant Y63F in complex with SAM -

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Basic information

Entry
Database: PDB / ID: 5n0n
TitleCrystal structure of OphA-DeltaC6 mutant Y63F 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
Chem-EDT / S-ADENOSYL-L-HOMOCYSTEINE / Methyltransferase/ribosomally synthesized cyclic peptide omphalotin A precursor ophMA
Similarity search - Component
Biological speciesOmphalotus olearius (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 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 1.2Jun 12, 2019Group: Data collection / Structure summary
Category: audit_author / database_PDB_rev / database_PDB_rev_record
Item: _audit_author.name
Revision 1.3Jan 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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 1.4Oct 23, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7535
Polymers45,0281
Non-polymers7254
Water4,666259
1
A: Peptide N-methyltransferase
hetero molecules

A: Peptide N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,50710
Polymers90,0562
Non-polymers1,4518
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_395-x-2,-y+4,z1
Unit cell
Length a, b, c (Å)87.304, 93.664, 165.331
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Peptide N-methyltransferase


Mass: 45028.191 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Omphalotus olearius (fungus) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2R2JFH4*PLUS
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-EDT / {[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID


Mass: 292.243 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O8
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / 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: 3.75 Å3/Da / Density % sol: 34.47 %
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: 1.76→82.67 Å / Num. obs: 67412 / % possible obs: 99.5 % / Redundancy: 5.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.032 / Net I/σ(I): 24
Reflection shellResolution: 1.76→1.79 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.752 / Mean I/σ(I) obs: 2.2 / CC1/2: 0.791 / % possible all: 99.5

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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: 1.76→82.67 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.964 / SU B: 4.068 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20022 3387 5 %RANDOM
Rwork0.18818 ---
obs0.18881 64025 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.589 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å20 Å2
2---1.51 Å20 Å2
3---1.63 Å2
Refinement stepCycle: 1 / Resolution: 1.76→82.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3069 0 48 259 3376
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0193285
X-RAY DIFFRACTIONr_bond_other_d0.0010.023011
X-RAY DIFFRACTIONr_angle_refined_deg1.2781.9824482
X-RAY DIFFRACTIONr_angle_other_deg0.93437004
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3715415
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.23823.916143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.85615521
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5651522
X-RAY DIFFRACTIONr_chiral_restr0.0760.2494
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213711
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02653
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_it0.9683.1561644
X-RAY DIFFRACTIONr_mcbond_other0.9683.1571643
X-RAY DIFFRACTIONr_mcangle_it1.7394.7172069
X-RAY DIFFRACTIONr_mcangle_other1.7394.7172070
X-RAY DIFFRACTIONr_scbond_it0.8663.3761641
X-RAY DIFFRACTIONr_scbond_other0.8663.3611639
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.5064.9952413
X-RAY DIFFRACTIONr_long_range_B_refined4.60337.2963448
X-RAY DIFFRACTIONr_long_range_B_other4.7936.6853396
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.756→1.802 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 262 -
Rwork0.283 4731 -
obs--99.9 %
Refinement TLS params.Method: refined / Origin x: -86.6069 Å / Origin y: 187.7831 Å / Origin z: 28.0843 Å
111213212223313233
T0.0546 Å20.0036 Å20.0054 Å2-0.0717 Å2-0.0011 Å2--0.0057 Å2
L0.4815 °2-0.1465 °2-0.0247 °2-1.3309 °2-0.1162 °2--0.5682 °2
S-0.0435 Å °0.0341 Å °0.0147 Å °-0.1661 Å °0.0842 Å °-0.0488 Å °-0.0004 Å °-0.001 Å °-0.0407 Å °

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