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- PDB-6gew: OphA Y63F-sinefungin complex -

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Basic information

Entry
Database: PDB / ID: 6gew
TitleOphA Y63F-sinefungin complex
ComponentsOphA
KeywordsTRANSFERASE / Peptide N-transferase
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
S-ADENOSYL-L-HOMOCYSTEINE / SINEFUNGIN / Methyltransferase/ribosomally synthesized cyclic peptide omphalotin A precursor ophMA
Similarity search - Component
Biological speciesOmphalotus olearius (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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
DepositionApr 27, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: OphA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7643
Polymers44,9981
Non-polymers7662
Water34219
1
A: OphA
hetero molecules

A: OphA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,5286
Polymers89,9962
Non-polymers1,5324
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area14550 Å2
ΔGint-80 kcal/mol
Surface area28160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.784, 89.784, 156.902
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein OphA


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 (bacteria) / References: UniProt: A0A2R2JFH4*PLUS
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N7O5
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 4.06 Å3/Da / Density % sol: 69.68 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.3-0.4 M KSCN, 0.1 M Bicine pH 8-9, 1.7-2.0 M Sodium malonate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 S 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: 2.1→77.76 Å / Num. obs: 43488 / % possible obs: 100 % / Redundancy: 10.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Net I/σ(I): 12.3
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 11 % / Rmerge(I) obs: 1.017 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2110 / CC1/2: 0.556 / % possible all: 98.64

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5N0O

5n0o


Resolution: 2.1→77.76 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.953 / SU B: 20.221 / SU ML: 0.216 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.149 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2581 2158 5 %RANDOM
Rwork0.2349 ---
obs0.23602 41277 99.93 %-
Solvent computationIon probe radii: 1.1 Å / Shrinkage radii: 1.1 Å / VDW probe radii: 1.3 Å
Displacement parametersBiso mean: 90.275 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20.24 Å20 Å2
2--0.47 Å20 Å2
3----1.53 Å2
Refinement stepCycle: 1 / Resolution: 2.1→77.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2929 0 53 19 3001
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0153055
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172734
X-RAY DIFFRACTIONr_angle_refined_deg1.0971.7994158
X-RAY DIFFRACTIONr_angle_other_deg0.4021.7496410
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1015372
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.66621.053133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.33115444
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1011519
X-RAY DIFFRACTIONr_chiral_restr0.0480.2403
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213402
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02551
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_it0.9554.7471507
X-RAY DIFFRACTIONr_mcbond_other0.9554.7471507
X-RAY DIFFRACTIONr_mcangle_it1.6847.1141875
X-RAY DIFFRACTIONr_mcangle_other1.6847.1121876
X-RAY DIFFRACTIONr_scbond_it0.7654.8611547
X-RAY DIFFRACTIONr_scbond_other0.7644.861548
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.3627.2472284
X-RAY DIFFRACTIONr_long_range_B_refined3.51356.543322
X-RAY DIFFRACTIONr_long_range_B_other3.5156.5223322
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.565 147 -
Rwork0.519 2987 -
obs--99.49 %
Refinement TLS params.Method: refined / Origin x: 42.4661 Å / Origin y: -0.6673 Å / Origin z: 24.7433 Å
111213212223313233
T0.5019 Å2-0.0099 Å2-0.0116 Å2-0.2596 Å2-0.0058 Å2--0.0013 Å2
L0.4821 °2-0.0597 °2-0.0603 °2-0.7997 °2-0.4653 °2--6.0971 °2
S-0.1921 Å °-0.0067 Å °0.0201 Å °-0.0367 Å °0.2271 Å °-0.007 Å °0.0708 Å °-0.4312 Å °-0.035 Å °

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