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- PDB-5n0r: Crystal structure of OphA-DeltaC6 mutant Y66F in complex with SAM -

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Basic information

Entry
Database: PDB / ID: 5n0r
TitleCrystal structure of OphA-DeltaC6 mutant Y66F in complex with SAM
ComponentsPeptide N-methyltransferase
KeywordsTRANSFERASE / methyltransferase
Function / homologyTetrapyrrole methylase / Tetrapyrrole (Corrin/Porphyrin) Methylases / Tetrapyrrole methylase, subdomain 1 / Tetrapyrrole methylase superfamily / methyltransferase activity / S-ADENOSYLMETHIONINE / Peptide N-methyltransferase
Function and homology information
Biological speciesOmphalotus olearius (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)45,7789
Polymers44,9981
Non-polymers7808
Water6,017334
1
A: Peptide N-methyltransferase
hetero molecules

A: Peptide N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,55618
Polymers89,9962
Non-polymers1,55916
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_395-x-2,-y+4,z1
Unit cell
Length a, b, c (Å)86.652, 93.355, 165.355
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-688-

HOH

21A-926-

HOH

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Components

#1: Protein Peptide N-methyltransferase


Mass: 44998.164 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: A0A2R2JFH9*PLUS
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 334 / 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: 3.72 Å3/Da / Density % sol: 66.91 %
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: 1.61→82.68 Å / Num. obs: 84772 / % possible obs: 98 % / Redundancy: 5.5 % / CC1/2: 1 / Rmerge(I) obs: 0.025 / Net I/σ(I): 27.6
Reflection shellResolution: 1.61→1.64 Å / Rmerge(I) obs: 0.609 / CC1/2: 0.842 / % possible all: 98

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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: 1.61→82.68 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.968 / SU B: 2.763 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.068 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19124 4197 5 %RANDOM
Rwork0.1776 ---
obs0.1783 80525 98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.849 Å2
Baniso -1Baniso -2Baniso -3
1--0.54 Å20 Å20 Å2
2---0.51 Å20 Å2
3---1.05 Å2
Refinement stepCycle: 1 / Resolution: 1.61→82.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3004 0 49 334 3387
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0193284
X-RAY DIFFRACTIONr_bond_other_d0.0010.023085
X-RAY DIFFRACTIONr_angle_refined_deg1.341.9844473
X-RAY DIFFRACTIONr_angle_other_deg0.91337159
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5915416
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.56623.83141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.89115530
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7671523
X-RAY DIFFRACTIONr_chiral_restr0.080.2502
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213682
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_it1.0012.9321648
X-RAY DIFFRACTIONr_mcbond_other1.0012.9321648
X-RAY DIFFRACTIONr_mcangle_it1.7614.3842071
X-RAY DIFFRACTIONr_mcangle_other1.7614.3842072
X-RAY DIFFRACTIONr_scbond_it1.0983.0571636
X-RAY DIFFRACTIONr_scbond_other1.0983.0571636
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.7934.5252402
X-RAY DIFFRACTIONr_long_range_B_refined4.53534.6363438
X-RAY DIFFRACTIONr_long_range_B_other4.29733.6483358
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.612→1.654 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 310 -
Rwork0.26 5930 -
obs--98.59 %
Refinement TLS params.Method: refined / Origin x: -86.4842 Å / Origin y: 187.4946 Å / Origin z: 27.9652 Å
111213212223313233
T0.0435 Å2-0.0177 Å2-0.0011 Å2-0.0139 Å2-0.0004 Å2--0.0235 Å2
L0.3838 °2-0.1221 °2-0.012 °2-1.2505 °2-0.0674 °2--0.4102 °2
S-0.0651 Å °0.0229 Å °0.0287 Å °-0.1542 Å °0.1062 Å °-0.0417 Å °-0.0147 Å °-0.0062 Å °-0.041 Å °

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