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- PDB-5w7p: Crystal structure of OxaC -

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Basic information

Entry
Database: PDB / ID: 5w7p
TitleCrystal structure of OxaC
ComponentsOxaC
KeywordsTRANSFERASE / methyltransferase / penicillium oxalicum / oxaline / indole alkaloid
Function / homology
Function and homology information


secondary metabolite biosynthetic process / O-methyltransferase activity / methylation
Similarity search - Function
O-methyltransferase domain / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / O-methyltransferase COMT-type / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / OxaC
Similarity search - Component
Biological speciesPenicillium oxalicum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 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: OxaC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6832
Polymers47,2851
Non-polymers3981
Water63135
1
A: OxaC
hetero molecules

A: OxaC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,3664
Polymers94,5692
Non-polymers7972
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_666-y+1,-x+1,-z+11
Buried area9240 Å2
ΔGint-85 kcal/mol
Surface area30540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.244, 162.244, 91.686
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422

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Components

#1: Protein OxaC


Mass: 47284.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penicillium oxalicum (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1B2TT09
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 3.44 Å3/Da / Density % sol: 64.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.6 / Details: lithium sulfate, ammonium sulfate, sodium citrate

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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 6M / Detector: PIXEL / Date: Jul 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→40.396 Å / Num. obs: 24188 / % possible obs: 99.96 % / Redundancy: 23.5 % / Biso Wilson estimate: 65.58 Å2 / Rmerge(I) obs: 0.0805 / Net I/σ(I): 24.28

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
XDSdata processing
XDSdata collection
RefinementMethod to determine structure: SAD / Resolution: 2.4→40.396 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 23.06
RfactorNum. reflection% reflection
Rfree0.2376 1213 5.02 %
Rwork0.1946 --
obs0.1966 24187 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 176.08 Å2 / Biso mean: 81.9977 Å2 / Biso min: 39.81 Å2
Refinement stepCycle: final / Resolution: 2.4→40.396 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3040 0 27 35 3102
Biso mean--80.13 67.93 -
Num. residues----396
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083133
X-RAY DIFFRACTIONf_angle_d0.9714251
X-RAY DIFFRACTIONf_chiral_restr0.058477
X-RAY DIFFRACTIONf_plane_restr0.006554
X-RAY DIFFRACTIONf_dihedral_angle_d5.8071887
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.4-2.49610.36621390.31224942633
2.4961-2.60970.2541440.248524992643
2.6097-2.74720.2571490.207625162665
2.7472-2.91930.26511340.222225102644
2.9193-3.14460.29141430.228125182661
3.1446-3.46090.2961090.214825692678
3.4609-3.96140.25921430.197525532696
3.9614-4.98940.20961420.167225762718
4.9894-40.40120.18651100.179727392849
Refinement TLS params.Method: refined / Origin x: 20.6622 Å / Origin y: 131.3332 Å / Origin z: 30.2509 Å
111213212223313233
T0.3957 Å20.1152 Å20.0306 Å2-0.7065 Å20.0408 Å2--0.495 Å2
L1.844 °2-0.0232 °2-0.5029 °2-1.126 °20.2241 °2--1.9634 °2
S0.0954 Å °0.7466 Å °-0.0689 Å °-0.1554 Å °-0.0053 Å °0.1702 Å °-0.0458 Å °-0.4597 Å °-0.0911 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA8 - 405
2X-RAY DIFFRACTION1allB1
3X-RAY DIFFRACTION1allC1 - 35

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