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- PDB-6qzz: full length OphA V404E in complex with SAH -

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Basic information

Entry
Database: PDB / ID: 6qzz
Titlefull length OphA V404E in complex with SAH
Components(Peptide N-methyltransferase) x 2
KeywordsTRANSFERASE / Peptide bond N-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: 1.85 Å
AuthorsSong, H. / Naismith, J.H.
CitationJournal: Acs Chem.Biol. / Year: 2020
Title: Substrate Plasticity of a Fungal Peptide alpha-N-Methyltransferase.
Authors: Song, H. / Fahrig-Kamarauskaite, J.R. / Matabaro, E. / Kaspar, H. / Shirran, S.L. / Zach, C. / Pace, A. / Stefanov, B.A. / Naismith, J.H. / Kunzler, M.
History
DepositionMar 12, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2020Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ncs_dom_lim
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_label_atom_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 2.1Jan 24, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptide N-methyltransferase
B: Peptide N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,1554
Polymers91,3862
Non-polymers7692
Water5,837324
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15370 Å2
ΔGint-90 kcal/mol
Surface area28560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.002, 91.723, 85.222
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / Refine code: 0

Dom-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1SAHSAHAA - C7 - 5016
2SERSERBB7 - 4126 - 411

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Components

#1: Protein Peptide N-methyltransferase


Mass: 45678.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Omphalotus olearius (fungus) / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A2R2JFI5*PLUS
#2: Protein Peptide N-methyltransferase


Mass: 45706.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Omphalotus olearius (fungus) / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A2R2JFI5*PLUS
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C14H20N6O5S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 324 / 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: 3.7 Å3/Da / Density % sol: 66.77 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.3-0.4 M KSCN, 0.1 M Bicine pH 9, 1.8-2.3 M Sodium malonate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.85→80.1 Å / Num. all: 798741 / Num. obs: 110277 / % possible obs: 100 % / Redundancy: 7.2 % / CC1/2: 1 / Rmerge(I) obs: 0.044 / Net I/σ(I): 16.9
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.766 / Mean I/σ(I) obs: 2 / Num. unique obs: 5363 / CC1/2: 0.621 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5N0O

5n0o


Resolution: 1.85→80.05 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.964 / SU B: 6.39 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.106 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22462 5568 5.1 %RANDOM
Rwork0.20638 ---
obs0.20731 104622 99.9 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 50.04 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å20 Å20 Å2
2---0.91 Å20 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.85→80.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6083 0 52 326 6461
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0136353
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175872
X-RAY DIFFRACTIONr_angle_refined_deg1.3931.6488660
X-RAY DIFFRACTIONr_angle_other_deg1.271.57413646
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7835792
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.0622.31316
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.355151014
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2211539
X-RAY DIFFRACTIONr_chiral_restr0.0630.2829
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027159
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021284
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_it4.413.0553177
X-RAY DIFFRACTIONr_mcbond_other4.413.0553177
X-RAY DIFFRACTIONr_mcangle_it5.3824.5493973
X-RAY DIFFRACTIONr_mcangle_other5.3824.5493974
X-RAY DIFFRACTIONr_scbond_it5.8673.5343176
X-RAY DIFFRACTIONr_scbond_other5.8673.5353176
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.9295.114688
X-RAY DIFFRACTIONr_long_range_B_refined9.72337.7787060
X-RAY DIFFRACTIONr_long_range_B_other9.72337.416986
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 12030 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 449 -
Rwork0.349 7547 -
obs--98.9 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.44810.06010.05962.4121-0.20780.7729-0.0449-0.00970.00170.08520.1168-0.4032-0.0151-0.0422-0.0720.0277-0.0099-0.01630.09330.00410.0883-27.51130.3144-21.3551
20.4165-0.10470.08222.3486-0.19380.6828-0.05860.01850.0185-0.08620.1297-0.38070.0393-0.0474-0.07110.0279-0.01080.00210.08750.00060.0828-27.5998-0.8479-21.6563
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 501
2X-RAY DIFFRACTION2B7 - 501

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