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- PDB-6mjf: Catalytic Domain of dbOphMA -

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Basic information

Entry
Database: PDB / ID: 6mjf
TitleCatalytic Domain of dbOphMA
ComponentsdbOphM
KeywordsBIOSYNTHETIC PROTEIN / Methyltransferase / borosin
Function / homology
Function and homology information


Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / methylation
Similarity search - Function
Tetrapyrrole methylase, N-terminal domain / Cobalt-precorrin-4 Transmethylase; domain 1 / Tetrapyrrole methylase / Tetrapyrrole (Corrin/Porphyrin) Methylases / Tetrapyrrole methylase, subdomain 1 / Tetrapyrrole methylase superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Methyltransferase/ribosomally synthesized cyclic peptide dendrothelin A precursor dbihMA
Similarity search - Component
Biological speciesDendrothele bispora CBS 962.96 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.198 Å
AuthorsOngpipatanakul, C. / Nair, S.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)S10 RR027109 A United States
CitationJournal: ACS Chem. Biol. / Year: 2018
Title: Molecular Basis for Autocatalytic Backbone N-Methylation in RiPP Natural Product Biosynthesis.
Authors: Ongpipattanakul, C. / Nair, S.K.
History
DepositionSep 20, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: dbOphM
B: dbOphM
C: dbOphM
D: dbOphM
E: dbOphM
F: dbOphM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)258,75011
Polymers256,8286
Non-polymers1,9225
Water11,620645
1
A: dbOphM
B: dbOphM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,3784
Polymers85,6092
Non-polymers7692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11590 Å2
ΔGint-77 kcal/mol
Surface area29850 Å2
MethodPISA
2
C: dbOphM
D: dbOphM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,3784
Polymers85,6092
Non-polymers7692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11660 Å2
ΔGint-76 kcal/mol
Surface area29850 Å2
MethodPISA
3
E: dbOphM
F: dbOphM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,9943
Polymers85,6092
Non-polymers3841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11620 Å2
ΔGint-72 kcal/mol
Surface area29490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.543, 109.543, 167.620
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
dbOphM


Mass: 42804.680 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dendrothele bispora CBS 962.96 (fungus)
Production host: Escherichia coli (E. coli) / References: UniProt: A0A452CSY8*PLUS
#2: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 645 / 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: 2.26 Å3/Da / Density % sol: 45.59 % / Description: Sheets.
Crystal growTemperature: 282.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2 mM SAH, 0.24 or 0.26 M NaF, 20- 26% PEG3350, and 0.1 M Bis-tris propane at pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97911 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 2.198→94.867 Å / Num. obs: 113414 / % possible obs: 99 % / Redundancy: 5.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.069 / Rsym value: 0.122 / Net I/σ(I): 10.4
Reflection shellResolution: 2.198→2.205 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.726 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1163 / CC1/2: 0.824 / Rpim(I) all: 0.498 / Rrim(I) all: 0.885 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(???)refinement
XDSdata reduction
XDSdata scaling
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.198→45.641 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 28.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.267 5842 5.15 %
Rwork0.231 --
obs0.2329 113366 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.198→45.641 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17336 0 130 645 18111
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00317913
X-RAY DIFFRACTIONf_angle_d0.62224394
X-RAY DIFFRACTIONf_dihedral_angle_d4.70210862
X-RAY DIFFRACTIONf_chiral_restr0.0442708
X-RAY DIFFRACTIONf_plane_restr0.0053195
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.198-2.2230.31592120.27883603X-RAY DIFFRACTION100
2.223-2.24920.3272000.27433634X-RAY DIFFRACTION100
2.2492-2.27660.36912280.28193616X-RAY DIFFRACTION100
2.2766-2.30540.29632170.27133545X-RAY DIFFRACTION100
2.3054-2.33570.31182420.26963584X-RAY DIFFRACTION100
2.3357-2.36770.2941920.26173603X-RAY DIFFRACTION100
2.3677-2.40160.27951710.26173612X-RAY DIFFRACTION100
2.4016-2.43740.32532080.26513687X-RAY DIFFRACTION100
2.4374-2.47550.31992120.27023533X-RAY DIFFRACTION100
2.4755-2.51610.32652100.26223555X-RAY DIFFRACTION99
2.5161-2.55950.29241950.25693629X-RAY DIFFRACTION99
2.5595-2.6060.35921600.25173562X-RAY DIFFRACTION98
2.606-2.65610.31011670.25893611X-RAY DIFFRACTION99
2.6561-2.71030.29751900.2613623X-RAY DIFFRACTION100
2.7103-2.76920.3171810.25493591X-RAY DIFFRACTION100
2.7692-2.83370.29072120.25483627X-RAY DIFFRACTION100
2.8337-2.90450.34681940.26393641X-RAY DIFFRACTION100
2.9045-2.9830.26581590.24353625X-RAY DIFFRACTION100
2.983-3.07080.2651790.2513630X-RAY DIFFRACTION100
3.0708-3.16990.30131500.24123628X-RAY DIFFRACTION99
3.1699-3.28310.25872030.24323627X-RAY DIFFRACTION99
3.2831-3.41450.30591610.23943617X-RAY DIFFRACTION99
3.4145-3.56990.2572040.22513563X-RAY DIFFRACTION99
3.5699-3.7580.28292030.21833590X-RAY DIFFRACTION99
3.758-3.99330.22192040.20983521X-RAY DIFFRACTION99
3.9933-4.30150.22652200.19033544X-RAY DIFFRACTION98
4.3015-4.73390.23711990.19743559X-RAY DIFFRACTION99
4.7339-5.4180.21942080.20673463X-RAY DIFFRACTION96
5.418-6.82240.25911810.22133511X-RAY DIFFRACTION97
6.8224-45.65110.21481800.20613390X-RAY DIFFRACTION94

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