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- PDB-6xm7: Crystal structure of DCA-S bound to Co-LSD4 from Sphingobium sp. ... -

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Basic information

Entry
Database: PDB / ID: 6xm7
TitleCrystal structure of DCA-S bound to Co-LSD4 from Sphingobium sp. strain SYK-6
ComponentsDioxygenase
KeywordsOXIDOREDUCTASE / lignostilbene dioxygenase / carotenoid cleavage dioxygenase / non-heme iron oxygenase / bacterial aromatic catabolism
Function / homologyOxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen / Carotenoid oxygenase / Retinal pigment epithelial membrane protein / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / metal ion binding / : / Chem-V5M / Dioxygenase
Function and homology information
Biological speciesSphingobium sp.
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsKuatsjah, E. / Chan, A.C. / Katahira, R. / Beckham, G.T. / Murphy, M.E. / Eltis, L.D.
Funding support Canada, 2items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)04802 Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)171359 Canada
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Structural and functional analysis of lignostilbene dioxygenases from Sphingobium sp. SYK-6.
Authors: Kuatsjah, E. / Chan, A.C.K. / Katahira, R. / Haugen, S.J. / Beckham, G.T. / Murphy, M.E.P. / Eltis, L.D.
History
DepositionJun 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 1.1May 26, 2021Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 21, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Oct 18, 2023Group: 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
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: Dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,26016
Polymers54,9741
Non-polymers1,28615
Water12,178676
1
A: Dioxygenase
hetero molecules

A: Dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,52132
Polymers109,9482
Non-polymers2,57330
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Unit cell
Length a, b, c (Å)85.320, 112.020, 114.670
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-815-

HOH

21A-1011-

HOH

31A-1141-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Dioxygenase / / LSD4


Mass: 54974.020 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingobium sp. (strain NBRC 103272 / SYK-6) (bacteria)
Strain: NBRC 103272 / SYK-6 / Gene: SLG_12860 / Production host: Escherichia coli (E. coli)
References: UniProt: G2IQT9, Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen

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Non-polymers , 5 types, 691 molecules

#2: Chemical ChemComp-V5M / (2E)-3-{4-hydroxy-3-[(E)-2-(4-hydroxy-3-methoxyphenyl)ethenyl]-5-methoxyphenyl}prop-2-enoic acid / Decarboxylated 8,5'-diferulic acid


Mass: 342.343 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H18O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Co / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 676 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.49 Å3/Da / Density % sol: 50.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.3 M magnesium acetate, 29% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 10, 2019
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.45→43.8 Å / Num. obs: 184209 / % possible obs: 97.8 % / Redundancy: 3.229 % / Biso Wilson estimate: 23.008 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.043 / Rrim(I) all: 0.052 / Χ2: 1.004 / Net I/σ(I): 15.68 / Num. measured all: 594735 / Scaling rejects: 4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.45-1.552.430.5031.947372434139303360.8540.63388.9
1.55-1.663.270.1915.829348228645285850.9690.22799.8
1.66-1.793.3410.09910.258473125386253590.9880.11899.9
1.79-1.943.4230.06315.527335021475214290.9940.07599.8
1.94-2.123.3670.04919.996166818355183140.9950.05899.8
2.12-2.353.4280.04223.675486816018160060.9960.0599.9
2.35-2.623.4340.03925.774215812291122750.9970.04699.9
2.62-2.983.4480.03528.453521410225102130.9970.04299.9
2.98-3.443.5570.03431.6127011760075940.9970.0499.9
3.44-4.073.3770.03233.0218895560455950.9970.03899.8
4.07-53.4840.03134.6513673392939240.9970.03799.9
5-43.83.4860.03234.3415961459645790.9970.03899.6

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Processing

Software
NameVersionClassification
PHENIX1.14-3260refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6OJR

6ojr


Resolution: 1.45→43.8 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1538 9207 5 %
Rwork0.1343 174946 -
obs0.1353 184153 97.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.06 Å2 / Biso mean: 22.9611 Å2 / Biso min: 10.79 Å2
Refinement stepCycle: final / Resolution: 1.45→43.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3856 0 128 676 4660
Biso mean--39.02 32.45 -
Num. residues----488
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.45-1.46650.39252470.3987461977
1.4665-1.48370.36272600.3583494883
1.4837-1.50180.36832760.3305520788
1.5018-1.52080.33682930.3133556192
1.5208-1.54080.30783070.3071583798
1.5408-1.5620.25373120.2314590699
1.562-1.58430.21553110.19865908100
1.5843-1.60790.18853160.16665950100
1.6079-1.6330.16543170.14895932100
1.633-1.65980.14793200.14026003100
1.6598-1.68840.16653100.13115901100
1.6884-1.71910.15663150.12715975100
1.7191-1.75220.17043080.12445945100
1.7522-1.7880.16093210.12115972100
1.788-1.82690.14633120.13125958100
1.8269-1.86940.15063140.12445943100
1.8694-1.91610.13053090.121593399
1.9161-1.96790.13643090.1175974100
1.9679-2.02580.14343150.11955944100
2.0258-2.09120.11793140.11255946100
2.0912-2.16590.13033120.1115996100
2.1659-2.25270.13683120.10885920100
2.2527-2.35520.13943110.11945949100
2.3552-2.47930.13893070.1195976100
2.4793-2.63470.1513050.11565938100
2.6347-2.8380.13353170.12295995100
2.838-3.12360.14713140.12835971100
3.1236-3.57540.16333160.12825920100
3.5754-4.50390.11993100.11535946100
4.5039-43.80.17073170.15745973100
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)
10.15340.1098-0.0330.537-0.22590.4071-0.00980.0150.0028-0.08710.01020.00370.0281-0.0062-00.12420.0002-0.00140.13520.00340.132618.433114.008233.9915
20.04110.02680.03460.0354-0.01090.06260.0622-0.0048-0.0772-0.0334-0.0699-0.096-0.00730.11450.00010.169-0.00160.00070.20460.0230.224531.991420.674843.8367
30.08350.0572-0.02530.1208-0.06960.17020.02-0.02460.00360.0853-0.0467-0.0369-0.07340.043800.143-0.0152-0.00430.1510.01190.159925.472420.431252.1599
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 358 )A2 - 358
2X-RAY DIFFRACTION2chain 'A' and (resid 359 through 393 )A359 - 393
3X-RAY DIFFRACTION3chain 'A' and (resid 394 through 489 )A394 - 489

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