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- PDB-6r00: OphA DeltaC6 V404F complex with SAH -

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Basic information

Entry
Database: PDB / ID: 6r00
TitleOphA DeltaC6 V404F complex with SAH
Components
  • PHE-PRO-TRP-MVA-ILE-MVA-PHE-GLY-VAL-ILE-GLY-VAL-ILE-GLY
  • Peptide N-methyltransferase
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: 1.74 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 / Refinement description / Category: citation / citation_author / software
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name / _software.name
Revision 1.3Jan 24, 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
Revision 1.4Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.mon_nstd_flag / _chem_comp.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptide N-methyltransferase
B: PHE-PRO-TRP-MVA-ILE-MVA-PHE-GLY-VAL-ILE-GLY-VAL-ILE-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9633
Polymers46,5792
Non-polymers3841
Water4,107228
1
A: Peptide N-methyltransferase
B: PHE-PRO-TRP-MVA-ILE-MVA-PHE-GLY-VAL-ILE-GLY-VAL-ILE-GLY
hetero molecules

A: Peptide N-methyltransferase
B: PHE-PRO-TRP-MVA-ILE-MVA-PHE-GLY-VAL-ILE-GLY-VAL-ILE-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,9276
Polymers93,1584
Non-polymers7692
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area17810 Å2
ΔGint-114 kcal/mol
Surface area28780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.772, 91.828, 162.999
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-679-

HOH

21A-726-

HOH

31A-824-

HOH

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Components

#1: Protein Peptide N-methyltransferase


Mass: 45048.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Omphalotus olearius (fungus) / Production host: Escherichia (bacteria) / References: UniProt: A0A2R2JFI5
#2: Protein/peptide PHE-PRO-TRP-MVA-ILE-MVA-PHE-GLY-VAL-ILE-GLY-VAL-ILE-GLY


Mass: 1530.893 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


Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 3.45 Å3/Da / Density % sol: 64.3 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.3-0.4 M KSCN, 0.1 M Bicine pH 9, 1.8-2.2 M Sodium malonate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.8 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: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.74→81.5 Å / Num. all: 733818 / Num. obs: 65997 / % possible obs: 100 % / Redundancy: 11.1 % / CC1/2: 1 / Rmerge(I) obs: 0.034 / Net I/σ(I): 32.8
Reflection shellResolution: 1.74→1.77 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.973 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3262 / CC1/2: 0.799 / % possible all: 99.4

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Processing

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

5n0o


Resolution: 1.74→81.5 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.966 / SU B: 3.691 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.079 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19206 3262 4.9 %RANDOM
Rwork0.17434 ---
obs0.17523 62734 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å
Displacement parametersBiso mean: 42.915 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å20 Å20 Å2
2--0.43 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.74→81.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3085 0 26 229 3340
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133215
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172972
X-RAY DIFFRACTIONr_angle_refined_deg1.4981.6484382
X-RAY DIFFRACTIONr_angle_other_deg1.3931.5736902
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9015400
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.47222.236161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.18115511
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.221520
X-RAY DIFFRACTIONr_chiral_restr0.0810.2419
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023634
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02657
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_it2.8392.8181608
X-RAY DIFFRACTIONr_mcbond_other2.7912.8131606
X-RAY DIFFRACTIONr_mcangle_it3.9144.2082010
X-RAY DIFFRACTIONr_mcangle_other3.9144.2082010
X-RAY DIFFRACTIONr_scbond_it3.8423.2061606
X-RAY DIFFRACTIONr_scbond_other3.8273.2051606
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6624.6452372
X-RAY DIFFRACTIONr_long_range_B_refined7.60234.3613560
X-RAY DIFFRACTIONr_long_range_B_other7.56333.9133516
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.742→1.787 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 218 -
Rwork0.257 4594 -
obs--100 %
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)
10.4329-0.1433-0.0041.3834-0.07480.4966-0.056-0.01630.0277-0.12880.0986-0.0717-0.0245-0.013-0.04260.0890.02730.00170.0290.00110.03730.33551.020827.6863
23.25610.4153-2.57854.313-0.81744.3496-0.20430.2305-0.0862-0.3546-0.11180.1203-0.1701-0.31050.31610.20960.0155-0.09820.1418-0.01610.1682-4.253318.48721.8815
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 501
2X-RAY DIFFRACTION2B398 - 411

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