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- PDB-6p29: N-demethylindolmycin synthase (PluN2) in complex with N-demethyli... -

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Basic information

Entry
Database: PDB / ID: 6p29
TitleN-demethylindolmycin synthase (PluN2) in complex with N-demethylindolmycin
ComponentsN-demethylindolmycin synthase (PluN2)
KeywordsBIOSYNTHETIC PROTEIN / N-demethylindolmycin synthase
Function / homologyGlyoxalase/fosfomycin resistance/dioxygenase domain / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / Chem-NQ7 / TRIETHYLENE GLYCOL / VOC domain-containing protein
Function and homology information
Biological speciesPseudoalteromonas luteoviolacea strain HI1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsDu, Y.L. / Higgins, M.A. / Zhao, G. / Ryan, K.S.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: Nat.Chem.Biol. / Year: 2019
Title: Convergent biosynthetic transformations to a bacterial specialized metabolite.
Authors: Du, Y.L. / Higgins, M.A. / Zhao, G. / Ryan, K.S.
History
DepositionMay 21, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2019Group: 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 1.2Oct 30, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 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: N-demethylindolmycin synthase (PluN2)
B: N-demethylindolmycin synthase (PluN2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3975
Polymers32,7602
Non-polymers6373
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5420 Å2
ΔGint-11 kcal/mol
Surface area10870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.070, 54.070, 176.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-354-

HOH

21A-355-

HOH

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Components

#1: Protein N-demethylindolmycin synthase (PluN2)


Mass: 16380.224 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudoalteromonas luteoviolacea strain HI1 (bacteria)
Gene: N473_05385 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A167HII1*PLUS
#2: Chemical ChemComp-NQ7 / (5S)-2-amino-5-[(1R)-1-(1H-indol-3-yl)ethyl]-1,3-oxazol-4(5H)-one


Mass: 243.261 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H13N3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 1.97 Å3/Da / Density % sol: 37.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M MgCl2, 0.1 M Bis-Tris buffer (pH 6.5), 0.2 M NDSB-201, 25 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jan 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.5→54.07 Å / Num. obs: 43152 / % possible obs: 100 % / Redundancy: 14.3 % / CC1/2: 0.985 / Net I/σ(I): 7.7
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 14.3 % / Mean I/σ(I) obs: 3.8 / Num. unique obs: 4198 / CC1/2: 0.906

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Processing

Software
NameClassification
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→46.135 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.91
RfactorNum. reflection% reflection
Rfree0.1956 2124 4.92 %
Rwork0.1676 --
obs0.169 43147 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→46.135 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2099 0 46 230 2375
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062248
X-RAY DIFFRACTIONf_angle_d0.8413054
X-RAY DIFFRACTIONf_dihedral_angle_d14.2071331
X-RAY DIFFRACTIONf_chiral_restr0.055338
X-RAY DIFFRACTIONf_plane_restr0.006398
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.53490.22521380.19462638X-RAY DIFFRACTION100
1.5349-1.57330.20211420.18082673X-RAY DIFFRACTION100
1.5733-1.61580.19011550.1782666X-RAY DIFFRACTION100
1.6158-1.66340.2171330.17772704X-RAY DIFFRACTION100
1.6634-1.71710.21241350.17272677X-RAY DIFFRACTION100
1.7171-1.77840.18991340.1652719X-RAY DIFFRACTION100
1.7784-1.84960.1941470.1662685X-RAY DIFFRACTION100
1.8496-1.93380.20671450.16782719X-RAY DIFFRACTION100
1.9338-2.03580.19831340.1642705X-RAY DIFFRACTION100
2.0358-2.16330.21271260.1672762X-RAY DIFFRACTION100
2.1633-2.33040.19821410.1642720X-RAY DIFFRACTION100
2.3304-2.56490.1821430.17362767X-RAY DIFFRACTION100
2.5649-2.93590.26691570.17462756X-RAY DIFFRACTION100
2.9359-3.69870.16481270.16192839X-RAY DIFFRACTION100
3.6987-46.15690.17091670.16012993X-RAY DIFFRACTION100
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)
11.27720.3151-0.17672.5141-0.79381.3776-0.00180.0205-0.09830.30560.0445-0.04780.03130.1345-0.03120.0301-0.003-0.02610.09840.01440.0817-11.64290.7997-10.4935
22.48770.2640.58394.1688-1.29692.7214-0.05080.12960.11470.0035-0.054-0.3433-0.02580.36790.03450.03360.0042-0.0210.13160.00950.1066-3.06466.3569-8.4592
31.8424-0.00450.97271.3823-1.71413.1352-0.01050.1214-0.11-0.0349-0.0198-0.12020.10650.12850.04370.05650.02190.00780.0788-0.00570.0916-8.82172.5839-13.8103
42.9924-0.7352-0.76050.98720.78181.6503-0.1030.199-0.05060.1632-0.0289-0.04250.0402-0.06260.02950.003-0.0062-0.0160.13230.0590.1165-17.180212.1074-19.1133
55.48481.9832.09934.05660.9727.21-0.0058-0.51740.12250.6081-0.06780.00430.0670.04840.03050.13080.0618-0.01670.17910.01190.0688-16.61099.09772.7044
61.7964-0.4129-0.36020.32781.13724.8484-0.1691-0.81070.8260.6198-0.1932-0.6861-1.39310.42340.3280.396-0.1089-0.17070.4372-0.05350.2715-9.921320.5609-1.1639
73.09510.8424-0.87940.9763-0.66071.33860.0007-0.27980.30610.53730.15620.1522-0.4698-0.3081-0.18070.1680.10160.05170.2160.0240.126-22.756114.9538-1.8478
82.44780.8784-1.82951.59750.33972.3507-0.111-0.41610.15020.57260.2030.32690.1213-0.5316-0.09930.22150.07470.06260.31160.04790.1396-23.580810.49863.7313
91.7963-0.37670.52111.0839-0.97471.6474-0.069-0.1966-0.16270.11360.28060.29010.0659-0.3865-0.1110.0529-0.00440.01070.19870.07770.1391-30.54435.4547-10.3978
101.978-1.06970.5231.0283-0.66492.98010.1960.3024-0.4052-0.2799-0.13880.25590.8578-0.2538-0.2420.1226-0.0555-0.06850.1558-0.01310.1668-22.0863-1.961-19.5604
114.1723-0.95933.09610.9244-0.24563.04340.39460.4457-0.7211-0.11690.04330.16140.52620.3691-0.40130.21020.0375-0.08190.1574-0.04530.2298-11.5468-10.2464-16.1949
122.2061-1.1202-0.15096.2803-1.15592.60490.11180.0952-0.33030.1202-0.0350.04430.3705-0.0735-0.02620.1031-0.029-0.05160.1070.00320.1372-21.0328-3.2577-16.7817
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 14 )
2X-RAY DIFFRACTION2chain 'A' and (resid 15 through 37 )
3X-RAY DIFFRACTION3chain 'A' and (resid 38 through 63 )
4X-RAY DIFFRACTION4chain 'A' and (resid 64 through 73 )
5X-RAY DIFFRACTION5chain 'A' and (resid 74 through 82 )
6X-RAY DIFFRACTION6chain 'A' and (resid 83 through 92 )
7X-RAY DIFFRACTION7chain 'A' and (resid 93 through 122 )
8X-RAY DIFFRACTION8chain 'A' and (resid 123 through 134 )
9X-RAY DIFFRACTION9chain 'B' and (resid 1 through 63 )
10X-RAY DIFFRACTION10chain 'B' and (resid 64 through 97 )
11X-RAY DIFFRACTION11chain 'B' and (resid 98 through 117 )
12X-RAY DIFFRACTION12chain 'B' and (resid 118 through 130 )

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