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- PDB-6xm8: Crystal structure of lignostilbene bound to Co-LSD4 from Sphingob... -

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Basic information

Entry
Database: PDB / ID: 6xm8
TitleCrystal structure of lignostilbene 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 / homologycarotenoid dioxygenase activity / carotene catabolic process / Carotenoid oxygenase / Retinal pigment epithelial membrane protein / Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen / metal ion binding / : / lignostilbene / Dioxygenase
Function and homology information
Biological speciesSphingobium sp.
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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)55,7209
Polymers54,9741
Non-polymers7468
Water12,250680
1
A: Dioxygenase
hetero molecules

A: Dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,44018
Polymers109,9482
Non-polymers1,49216
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Unit cell
Length a, b, c (Å)85.700, 112.540, 115.520
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-740-

HOH

21A-1070-

HOH

31A-1140-

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, 688 molecules

#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-V5P / lignostilbene / 4,4'-[(E)-ethene-1,2-diyl]bis(2-methoxyphenol)


Mass: 272.296 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H16O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#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


Mass: 18.015 Da / Num. of mol.: 680 / 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: 2.53 Å3/Da / Density % sol: 51.45 %
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: 08B1-1 / Wavelength: 0.97934 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jul 7, 2019
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.85→40.305 Å / Num. obs: 92163 / % possible obs: 100 % / Redundancy: 3.819 % / Biso Wilson estimate: 21.739 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.154 / Rrim(I) all: 0.18 / Χ2: 0.943 / Net I/σ(I): 6.66 / Num. measured all: 351935 / Scaling rejects: 9
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
1.85-1.963.7930.732.135550914636146330.7080.854100
1.96-2.093.8030.463.255169113595135920.8480.537100
2.09-2.233.8260.3244.374333211328113260.9210.377100
2.23-2.393.8240.2415.5137671985298510.9490.281100
2.39-2.583.8520.1946.5133772876887670.960.226100
2.58-2.813.8450.1527.7529496767176710.9740.176100
2.81-3.083.8290.1249.2824244633363320.9810.145100
3.08-3.43.8310.09911.0319697514151410.9880.115100
3.4-3.813.7890.08612.716303430343030.9880.099100
3.81-4.323.7850.07613.7512514330733060.990.089100
4.32-53.8180.07414.459782256225620.9920.085100
5-40.3053.8310.07314.0517924468846790.990.08599.8

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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: 1.85→40.305 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 16.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1732 4601 4.99 %
Rwork0.1466 87536 -
obs0.1479 92137 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 98.78 Å2 / Biso mean: 20.8738 Å2 / Biso min: 7.68 Å2
Refinement stepCycle: final / Resolution: 1.85→40.305 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3832 0 88 680 4600
Biso mean--38.8 29.57 -
Num. residues----483
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.85-1.8710.3431540.2772936100
1.871-1.8930.27471490.2442929100
1.893-1.91610.22521520.23192882100
1.9161-1.94040.26241540.21262964100
1.9404-1.96590.23821500.19452854100
1.9659-1.99280.2371600.18523009100
1.9928-2.02130.20531500.18042874100
2.0213-2.05150.21691500.17042890100
2.0515-2.08350.20421580.16612975100
2.0835-2.11770.18591510.15762871100
2.1177-2.15420.16471530.15622903100
2.1542-2.19330.16221540.14922899100
2.1933-2.23550.16751550.14512950100
2.2355-2.28120.1551550.14012952100
2.2812-2.33080.16081500.13442890100
2.3308-2.3850.19651500.13182914100
2.385-2.44460.15651520.13262942100
2.4446-2.51070.14491570.13472885100
2.5107-2.58460.16631530.13432915100
2.5846-2.6680.19211570.13512925100
2.668-2.76330.16691560.13842959100
2.7633-2.87390.15991540.13212888100
2.8739-3.00470.1671550.13652888100
3.0047-3.1630.15121510.14092951100
3.163-3.36110.17261510.1322904100
3.3611-3.62050.17511530.12922920100
3.6205-3.98450.14371540.11952949100
3.9845-4.56040.10931550.1092909100
4.5604-5.7430.13291540.12672917100
5.743-40.3050.21631540.1852289299
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)
10.18680.03460.02470.4673-0.13870.30930.00270.01470.0032-0.06910.00620.04890.0355-0.02690.00010.0919-0.0051-0.00640.10910.00470.104313.97619.697338.5286
20.07280.07570.03140.0779-0.04450.0976-0.0310.11420.0186-0.26970.03370.02650.0415-0.017100.1962-0.00220.01130.1530.0270.133220.613218.126819.6743
30.03320.065-0.02030.07140.010.14590.00630.02530.0041-0.0653-0.0489-0.1305-0.07640.062-0.02740.1332-0.00280.02390.13550.02820.15431.018221.312129.2739
4-0.00090.03140.05780.06670.00170.04160.0179-0.01030.0021-0.0177-0.0371-0.0027-0.12590.079-0.01820.1457-0.02020.00990.14570.02470.135727.050529.724135.4392
50.074-0.0751-0.01520.16490.07880.137-0.00710.07180.0046-0.1611-0.0399-0.1856-0.09080.14220.00090.121-0.04080.01060.1860.04730.223837.404821.116645.4893
60.09820.0904-0.0770.1166-0.15170.23010.024-0.02540.02310.0665-0.0536-0.0156-0.06220.0391-0.03850.1049-0.0225-0.00720.11670.00990.122724.638819.107453.4323
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 237 )A2 - 237
2X-RAY DIFFRACTION2chain 'A' and (resid 238 through 277 )A238 - 277
3X-RAY DIFFRACTION3chain 'A' and (resid 278 through 333 )A278 - 333
4X-RAY DIFFRACTION4chain 'A' and (resid 334 through 373 )A334 - 373
5X-RAY DIFFRACTION5chain 'A' and (resid 374 through 404 )A374 - 404
6X-RAY DIFFRACTION6chain 'A' and (resid 405 through 489 )A405 - 489

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