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- PDB-5ouf: Crystal structure of OphA-DeltaC6 mutant W400A in complex with Si... -

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Basic information

Entry
Database: PDB / ID: 5ouf
TitleCrystal structure of OphA-DeltaC6 mutant W400A in complex with Sinefungin
ComponentsOphA peptide 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 / THIOCYANATE ION / SINEFUNGIN / Methyltransferase/ribosomally synthesized cyclic peptide omphalotin A precursor ophMA
Similarity search - Component
Biological speciesOmphalotus olearius (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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
DepositionAug 23, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 5, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Nov 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: OphA peptide N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5887
Polymers44,9131
Non-polymers6756
Water3,297183
1
A: OphA peptide N-methyltransferase
hetero molecules

A: OphA peptide N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,17614
Polymers89,8262
Non-polymers1,34912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_995-x+4,-y+4,z1
Unit cell
Length a, b, c (Å)85.540, 91.940, 162.010
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-666-

HOH

21A-715-

HOH

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Components

#1: Protein OphA 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
#2: Chemical ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N7O5
#3: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO3
#4: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CNS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 3.55 Å3/Da / Density % sol: 65.31 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.3-0.4 M KSCN, 0.1 M Bicine pH 8.5, 1.3-1.5 M sodium malonate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.7 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7 Å / Relative weight: 1
ReflectionResolution: 1.7→49.55 Å / Num. obs: 70395 / % possible obs: 100 % / Redundancy: 7.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Net I/σ(I): 14.1
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 7.7 % / Rmerge(I) obs: 1.73 / Mean I/σ(I) obs: 1.2 / CC1/2: 0.47 / % possible all: 100

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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: 1.7→49.55 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.967 / SU B: 4.165 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.074 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19155 3533 5 %RANDOM
Rwork0.16506 ---
obs0.16639 66862 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.3 Å
Displacement parametersBiso mean: 40.921 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20 Å20 Å2
2--0.83 Å20 Å2
3----1.16 Å2
Refinement stepCycle: 1 / Resolution: 1.7→49.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3010 0 43 183 3236
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193183
X-RAY DIFFRACTIONr_bond_other_d0.0020.022941
X-RAY DIFFRACTIONr_angle_refined_deg1.3741.9824330
X-RAY DIFFRACTIONr_angle_other_deg0.92636834
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9465397
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.66423.813139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.0515511
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7931522
X-RAY DIFFRACTIONr_chiral_restr0.0830.2481
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213554
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02631
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_it1.733.3321591
X-RAY DIFFRACTIONr_mcbond_other1.7253.3281587
X-RAY DIFFRACTIONr_mcangle_it2.3954.9871989
X-RAY DIFFRACTIONr_mcangle_other2.3954.9861990
X-RAY DIFFRACTIONr_scbond_it1.8753.631591
X-RAY DIFFRACTIONr_scbond_other1.8613.6221585
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3815.3192335
X-RAY DIFFRACTIONr_long_range_B_refined3.2240.1273480
X-RAY DIFFRACTIONr_long_range_B_other3.17539.9233457
X-RAY DIFFRACTIONr_rigid_bond_restr1.67436121
X-RAY DIFFRACTIONr_sphericity_free29.9055120
X-RAY DIFFRACTIONr_sphericity_bonded12.32856114
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 242 -
Rwork0.294 4948 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 170.8349 Å / Origin y: 184.6698 Å / Origin z: 215.4435 Å
111213212223313233
T0.0094 Å2-0.0002 Å20.002 Å2-0.0058 Å2-0.0015 Å2--0.1084 Å2
L0.1151 °20.0729 °20.0412 °2-0.5113 °2-0.0128 °2--0.0846 °2
S-0.0146 Å °0.0232 Å °-0.0033 Å °0.0438 Å °0.0359 Å °0.0174 Å °0.0003 Å °0.0088 Å °-0.0213 Å °

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