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- PDB-5n4i: Crystal structure of OphA-DeltaC6 mutant W400A in complex with SAM -

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Basic information

Entry
Database: PDB / ID: 5n4i
TitleCrystal structure of OphA-DeltaC6 mutant W400A 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
BICARBONATE ION / MALONATE ION / S-ADENOSYLMETHIONINE / THIOCYANATE ION / Methyltransferase/ribosomally synthesized cyclic peptide omphalotin A precursor ophMA
Similarity search - Component
Biological speciesOmphalotus olearius (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 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 10, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2018Group: Data collection / Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_special_symmetry
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 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)45,7999
Polymers44,9131
Non-polymers8868
Water4,234235
1
A: Peptide N-methyltransferase
hetero molecules

A: Peptide N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,59818
Polymers89,8262
Non-polymers1,77216
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_395-x-2,-y+4,z1
Unit cell
Length a, b, c (Å)85.885, 91.951, 162.181
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-502-

GOL

21A-831-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Peptide N-methyltransferase


Mass: 44913.059 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: A0A2R2JFI9*PLUS

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Non-polymers , 6 types, 243 molecules

#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / 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: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CNS
#5: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#6: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.46 Å3/Da / Density % sol: 64.42 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.3-0.4 M KSCN, 0.1 M Bicine pH 9.0, 1.7-1.9 M sodium malonate

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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: 1.59→75.9 Å / Num. obs: 85158 / % possible obs: 98.6 % / Redundancy: 7.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.045 / Net I/σ(I): 14.9
Reflection shellResolution: 1.59→1.62 Å / Redundancy: 7.2 % / Rmerge(I) obs: 1.545 / Mean I/σ(I) obs: 1.2 / CC1/2: 0.605 / % possible all: 95.3

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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: 1.59→75.9 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.969 / SU B: 4.699 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20328 4159 5 %RANDOM
Rwork0.17253 ---
obs0.17411 79834 97.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.61 Å2
Baniso -1Baniso -2Baniso -3
1--1.32 Å20 Å20 Å2
2---0.54 Å20 Å2
3---1.86 Å2
Refinement stepCycle: 1 / Resolution: 1.59→75.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3042 0 56 235 3333
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193280
X-RAY DIFFRACTIONr_bond_other_d0.0020.023013
X-RAY DIFFRACTIONr_angle_refined_deg1.3291.9844471
X-RAY DIFFRACTIONr_angle_other_deg0.9337012
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.175415
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.47924.028144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.72515524
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7041522
X-RAY DIFFRACTIONr_chiral_restr0.0840.2494
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213709
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02648
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_it1.9693.1621642
X-RAY DIFFRACTIONr_mcbond_other1.9383.1571638
X-RAY DIFFRACTIONr_mcangle_it2.4214.7222065
X-RAY DIFFRACTIONr_mcangle_other2.4214.7212066
X-RAY DIFFRACTIONr_scbond_it1.9723.4141637
X-RAY DIFFRACTIONr_scbond_other1.9713.4081635
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3015.0222406
X-RAY DIFFRACTIONr_long_range_B_refined3.40538.6923630
X-RAY DIFFRACTIONr_long_range_B_other3.16838.1353579
X-RAY DIFFRACTIONr_rigid_bond_restr1.01136290
X-RAY DIFFRACTIONr_sphericity_free30.3815140
X-RAY DIFFRACTIONr_sphericity_bonded7.76756310
LS refinement shellResolution: 1.589→1.631 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.463 293 -
Rwork0.408 5585 -
obs--92.65 %
Refinement TLS params.Method: refined / Origin x: -85.4731 Å / Origin y: 184.457 Å / Origin z: 27.4105 Å
111213212223313233
T0.0817 Å2-0.0115 Å2-0.001 Å2-0.0154 Å2-0.0043 Å2--0.0196 Å2
L0.319 °2-0.1322 °20 °2-1.1826 °2-0.0977 °2--0.3031 °2
S-0.0666 Å °-0.0067 Å °0.029 Å °-0.1778 Å °0.1212 Å °-0.0468 Å °-0.0084 Å °-0.0142 Å °-0.0546 Å °

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