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- PDB-6xm9: Crystal structure of vanillin bound to Co-LSD4 from Sphingobium s... -

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Basic information

Entry
Database: PDB / ID: 6xm9
TitleCrystal structure of vanillin 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 / homology
Function and homology information


carotenoid dioxygenase activity / carotene catabolic process / Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen / metal ion binding
Similarity search - Function
Carotenoid oxygenase / Retinal pigment epithelial membrane protein
Similarity search - Domain/homology
ACETATE ION / : / 4-hydroxy-3-methoxybenzaldehyde / Dioxygenase
Similarity search - Component
Biological speciesSphingobium sp.
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.651 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)55,97715
Polymers54,9741
Non-polymers1,00314
Water12,629701
1
A: Dioxygenase
hetero molecules

A: Dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,95430
Polymers109,9482
Non-polymers2,00528
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Unit cell
Length a, b, c (Å)85.160, 112.157, 115.311
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-697-

HOH

21A-970-

HOH

31A-1144-

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 , 6 types, 715 molecules

#2: Chemical ChemComp-V55 / 4-hydroxy-3-methoxybenzaldehyde / p-vanillin


Mass: 152.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


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


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 701 / 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: 2.5 Å3/Da / Density % sol: 50.88 %
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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 127993 / % possible obs: 100 % / Redundancy: 7.8 % / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.043 / Rrim(I) all: 0.131 / Χ2: 1.152 / Net I/σ(I): 9.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.65-1.684.10.58432450.8080.3260.6720.76999.7
1.68-1.714.40.57233050.8390.3070.6520.767100
1.71-1.744.70.52132780.8790.2690.5880.798100
1.74-1.784.90.45133050.9020.2260.5060.822100
1.78-1.825.10.41432720.9340.2020.4620.863100
1.82-1.865.30.35733060.9480.1710.3970.905100
1.86-1.95.50.30832730.9620.1440.3410.997100
1.9-1.965.70.26932880.9670.1220.2961.178100
1.96-2.016.30.2633090.970.110.2831.464100
2.01-2.087.20.25832990.9720.1010.2771.61100
2.08-2.157.60.23632950.9780.090.2531.349100
2.15-2.247.90.21733120.9780.0810.2321.313100
2.24-2.348.30.20433100.9830.0740.2171.294100
2.34-2.468.90.18833260.9820.0660.1991.237100
2.46-2.629.80.17333020.9860.0580.1821.313100
2.62-2.8211.70.15533390.9910.0470.1621.284100
2.82-3.1112.10.12833440.9930.0380.1341.181100
3.11-3.5512.10.10133540.9960.030.1061.196100
3.55-4.48120.07634060.9980.0230.081.076100
4.48-5011.60.05835080.9980.0170.0610.83699.7

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Processing

Software
NameVersionClassification
PHENIX1.14-3260refinement
DENZOdata reduction
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6OJR

6ojr


Resolution: 1.651→29.712 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 18.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1868 6489 5.1 %
Rwork0.1589 120857 -
obs0.1604 127346 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.73 Å2 / Biso mean: 18.261 Å2 / Biso min: 5.92 Å2
Refinement stepCycle: final / Resolution: 1.651→29.712 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3805 0 102 701 4608
Biso mean--41.24 28.32 -
Num. residues----479
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.651-1.66930.27361900.2543386895
1.6693-1.6890.25072400.241399899
1.689-1.70960.2912240.2254063100
1.7096-1.73120.23362430.21373991100
1.7312-1.7540.20382190.2074103100
1.754-1.7780.24391980.1994078100
1.778-1.80340.22332130.2033998100
1.8034-1.83030.2272160.18734089100
1.8303-1.85890.22412200.18944082100
1.8589-1.88940.19812360.18094070100
1.8894-1.9220.21712170.1813975100
1.922-1.95690.20062250.16744050100
1.9569-1.99450.19532180.17154026100
1.9945-2.03520.21092220.16984098100
2.0352-2.07950.17482190.15794068100
2.0795-2.12780.20312320.15734049100
2.1278-2.1810.22531930.14914030100
2.181-2.240.19621930.14834077100
2.24-2.30590.16942270.14794040100
2.3059-2.38030.19362220.14484025100
2.3803-2.46530.15671960.1461409799
2.4653-2.5640.20232040.1504398799
2.564-2.68060.20332310.1486403499
2.6806-2.82180.18752190.1549396398
2.8218-2.99840.17792000.1513399898
2.9984-3.22970.15961910.1461399698
3.2297-3.55420.14682170.1392400099
3.5542-4.06740.14361960.1269402799
4.0674-5.12030.15062650.1235393498
5.1203-29.7120.20392030.1852404399
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)
10.0640.0696-0.10840.1076-0.10490.2485-0.01060.0093-0.02060.0152-0.073-0.1041-0.11560.0836-0.01530.0878-0.03140.00110.12130.02950.140231.41525.970544.717
20.10140.1886-0.10420.3262-0.34120.3930.0438-0.0203-0.00410.0936-0.0661-0.0246-0.07330.0519-0.00550.0811-0.0165-0.00530.09160.00780.091924.418719.070453.4224
30.11820.02460.0730.5612-0.28570.46320.00510.00810.0019-0.07730.02840.07140.0536-0.02350.03470.0641-0.007-0.01070.08140.00460.083413.70369.817338.4948
40.15890.18420.00960.1906-0.1030.2778-0.01170.11810.0335-0.28010.00690.01150.0896-0.0225-0.00190.16770.00210.00860.12710.01920.104120.482918.14819.6378
50.1050.2185-0.07940.2629-0.12630.4063-0.0024-0.0071-0.0393-0.0533-0.0353-0.0574-0.05790.0931-0.01440.0913-0.0030.01820.11840.0240.112830.346423.601329.617
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 359 through 404 )A359 - 404
2X-RAY DIFFRACTION2chain 'A' and (resid 405 through 489 )A405 - 489
3X-RAY DIFFRACTION3chain 'A' and (resid 2 through 237 )A2 - 237
4X-RAY DIFFRACTION4chain 'A' and (resid 238 through 277 )A238 - 277
5X-RAY DIFFRACTION5chain 'A' and (resid 278 through 358 )A278 - 358

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