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- PDB-5n0u: Crystal structure of OphA-DeltaC6 mutant R72A in complex with SAH -

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Basic information

Entry
Database: PDB / ID: 5n0u
TitleCrystal structure of OphA-DeltaC6 mutant R72A 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: 1.68 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 1.2May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptide N-Methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3966
Polymers44,9141
Non-polymers4825
Water4,558253
1
A: Peptide N-Methyltransferase
hetero molecules

A: Peptide N-Methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,79112
Polymers89,8282
Non-polymers96310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_365-x-2,-y+1,z1
Buried area15400 Å2
ΔGint-162 kcal/mol
Surface area30080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.086, 91.881, 164.436
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: 44914.023 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: A0A2R2JFI2*PLUS
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 3.62 Å3/Da / Density % sol: 66.02 %
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: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.68→49.92 Å / Num. obs: 74443 / % possible obs: 99.9 % / Redundancy: 9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.083 / Net I/σ(I): 10.8
Reflection shellResolution: 1.68→1.71 Å / Redundancy: 8.6 % / Rmerge(I) obs: 1.713 / Mean I/σ(I) obs: 1 / CC1/2: 0.515 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.68→49.92 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.961 / SU B: 4.784 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21709 3789 5.1 %RANDOM
Rwork0.1963 ---
obs0.19729 69990 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.862 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å20 Å20 Å2
2---1.13 Å20 Å2
3---1.46 Å2
Refinement stepCycle: 1 / Resolution: 1.68→49.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3023 0 30 253 3306
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193178
X-RAY DIFFRACTIONr_bond_other_d0.0020.022933
X-RAY DIFFRACTIONr_angle_refined_deg1.3651.9784337
X-RAY DIFFRACTIONr_angle_other_deg0.90836816
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9955401
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.46524.286140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.35915510
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3071519
X-RAY DIFFRACTIONr_chiral_restr0.0770.2482
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213570
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02619
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_it1.1143.0151595
X-RAY DIFFRACTIONr_mcbond_other1.1143.0151594
X-RAY DIFFRACTIONr_mcangle_it1.9564.5071999
X-RAY DIFFRACTIONr_mcangle_other1.9554.5062000
X-RAY DIFFRACTIONr_scbond_it1.0963.1471582
X-RAY DIFFRACTIONr_scbond_other1.0963.1471582
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8594.6782338
X-RAY DIFFRACTIONr_long_range_B_refined5.6236.5243534
X-RAY DIFFRACTIONr_long_range_B_other5.49336.0453491
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.679→1.723 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.418 276 -
Rwork0.392 4944 -
obs--95.53 %
Refinement TLS params.Method: refined / Origin x: -86.3894 Å / Origin y: 45.5724 Å / Origin z: 27.628 Å
111213212223313233
T0.0683 Å20.0179 Å20 Å2-0.0456 Å20.0018 Å2--0.0039 Å2
L0.7134 °2-0.191 °2-0.0038 °2-1.5903 °20.1249 °2--0.5087 °2
S-0.0937 Å °-0.0159 Å °-0.0311 Å °-0.1811 Å °0.0928 Å °0.0533 Å °-0.0006 Å °-0.0003 Å °0.0009 Å °

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