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- PDB-5w7k: Crystal structure of OxaG -

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Basic information

Entry
Database: PDB / ID: 5w7k
TitleCrystal structure of OxaG
ComponentsOxaG
KeywordsTRANSFERASE / methyltransferase / penicillium oxalicum / oxaline / indole alkaloid
Function / homologyMethyltransferase domain 25 / Methyltransferase domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily / S-ADENOSYL-L-HOMOCYSTEINE / OxaG
Function and homology information
Biological speciesPenicillium oxalicum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.994 Å
AuthorsNewmister, S.A. / Romminger, S. / Schmidt, J.J. / Williams, R.M. / Smith, J.L. / Berlinck, R.G.S. / Sherman, D.H.
Funding support United States, Brazil, 6items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA070375 United States
National Science Foundation (NSF, United States)CHE 1220121 United States
Sao Paulo Research Foundation (FAPESP)2012/50026-3 Brazil
Sao Paulo Research Foundation (FAPESP)2013/50228-8 Brazil
Sao Paulo Research Foundation (FAPESP)2014/05670-7 Brazil
CAPESBEX 4498/14-3 Brazil
CitationJournal: Org. Biomol. Chem. / Year: 2018
Title: Unveiling sequential late-stage methyltransferase reactions in the meleagrin/oxaline biosynthetic pathway.
Authors: Newmister, S.A. / Romminger, S. / Schmidt, J.J. / Williams, R.M. / Smith, J.L. / Berlinck, R.G.S. / Sherman, D.H.
History
DepositionJun 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 5, 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Sep 26, 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 1.3Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 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

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Assembly

Deposited unit
A: OxaG
B: OxaG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,6005
Polymers69,7952
Non-polymers8043
Water2,126118
1
A: OxaG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2822
Polymers34,8981
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: OxaG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3183
Polymers34,8981
Non-polymers4202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)121.628, 36.208, 126.304
Angle α, β, γ (deg.)90.000, 102.830, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-466-

HOH

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Components

#1: Protein OxaG


Mass: 34897.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penicillium oxalicum (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1B2TT18
#2: 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: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 1.94 Å3/Da / Density % sol: 36.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.7 / Details: PEG 3350, MPD, magnesium chloride, bis-tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.99→49.315 Å / Num. obs: 36979 / % possible obs: 99.13 % / Redundancy: 6.4 % / Biso Wilson estimate: 35.44 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.124 / Net I/σ(I): 9.84

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
XDSdata processing
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
XDSdata collection
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.994→49.315 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.11
RfactorNum. reflection% reflection
Rfree0.2595 1828 4.94 %
Rwork0.2204 --
obs0.2223 36977 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 111.92 Å2 / Biso mean: 45.7124 Å2 / Biso min: 17.65 Å2
Refinement stepCycle: final / Resolution: 1.994→49.315 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4209 0 53 118 4380
Biso mean--41.57 44.87 -
Num. residues----543
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084365
X-RAY DIFFRACTIONf_angle_d0.9685949
X-RAY DIFFRACTIONf_chiral_restr0.055694
X-RAY DIFFRACTIONf_plane_restr0.006730
X-RAY DIFFRACTIONf_dihedral_angle_d4.6192583
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.994-2.04790.33681340.32022478261292
2.0479-2.10820.31351550.27942677283299
2.1082-2.17620.31391280.26452681280999
2.1762-2.2540.28741120.267727432855100
2.254-2.34420.32051490.272926662815100
2.3442-2.45090.32711330.269926952828100
2.4509-2.58010.31541440.274927032847100
2.5801-2.74180.2921340.263327082842100
2.7418-2.95340.28491280.232727292857100
2.9534-3.25060.24941370.22527332870100
3.2506-3.72080.24141580.196327452903100
3.7208-4.68730.2261560.181727362892100
4.6873-49.32970.22571600.187928553015100

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