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- PDB-6xm6: Crystal structure of cobalt-bound LSD4 from Sphingobium sp. strai... -

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Basic information

Entry
Database: PDB / ID: 6xm6
TitleCrystal structure of cobalt-bound 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 / : / 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)55,0332
Polymers54,9741
Non-polymers591
Water14,124784
1
A: Dioxygenase
hetero molecules

A: Dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,0664
Polymers109,9482
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Unit cell
Length a, b, c (Å)85.480, 112.180, 114.740
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-727-

HOH

21A-1231-

HOH

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Components

#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
#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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 784 / Source method: isolated from a natural source / Formula: H2O
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: 50.83 %
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→43.847 Å / Num. obs: 188761 / % possible obs: 99.9 % / Redundancy: 3.33 % / Biso Wilson estimate: 22.45 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.051 / Rrim(I) all: 0.061 / Χ2: 1.024 / Net I/σ(I): 14.02 / Num. measured all: 628528
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
1.45-1.553.1530.3853.0410769534282341590.9210.46699.6
1.55-1.663.320.1537.179547928781287580.9740.18399.9
1.66-1.793.3140.08611.288427725465254330.9880.10399.9
1.79-1.943.3660.06315.267271121612216000.9920.07599.9
1.94-2.123.440.05518.526320418389183710.9920.06599.9
2.12-2.353.3470.05120.185379316093160710.9930.0699.9
2.35-2.623.4280.04721.84224912337123240.9930.05699.9
2.62-2.983.4440.04523.223531510258102530.9940.054100
2.98-3.443.3160.04324.1425297763776280.9950.05199.9
3.44-4.073.3980.04125.3719090562356180.9940.04999.9
4.07-53.4870.04126.1513751394539440.9950.049100
5-43.8473.4040.04125.6915667461646020.9960.04899.7

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Processing

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

6ojr


Resolution: 1.45→43.847 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 15.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1589 9407 4.98 %
Rwork0.1389 179317 -
obs0.1399 188724 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.75 Å2 / Biso mean: 20.612 Å2 / Biso min: 8.13 Å2
Refinement stepCycle: final / Resolution: 1.45→43.847 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3841 0 1 784 4626
Biso mean--12.23 30.74 -
Num. residues----484
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.45-1.46640.80093130.72185939100
1.4664-1.48370.57853140.5487595599
1.4837-1.50180.3983170.4285592699
1.5018-1.52080.313100.31445960100
1.5208-1.54080.27563120.24676040100
1.5408-1.56190.22793160.20235956100
1.5619-1.58420.19543150.17565954100
1.5842-1.60790.1763150.14935987100
1.6079-1.6330.15733170.13395969100
1.633-1.65980.15993120.12966009100
1.6598-1.68840.14773180.13035970100
1.6884-1.71910.16143140.12725991100
1.7191-1.75220.16373100.13485930100
1.7522-1.78790.16313160.13046030100
1.7879-1.82680.16193110.1395949100
1.8268-1.86930.163080.13545964100
1.8693-1.9160.15083130.14095988100
1.916-1.96780.16593160.13476018100
1.9678-2.02580.14753130.13135947100
2.0258-2.09110.16323170.12436013100
2.0911-2.16590.15113160.11566011100
2.1659-2.25260.11643120.11135902100
2.2526-2.35510.13853140.12176007100
2.3551-2.47930.13083120.11685985100
2.4793-2.63460.15323030.11765978100
2.6346-2.8380.14373160.11936004100
2.838-3.12350.1593130.12965981100
3.1235-3.57530.13553120.12595973100
3.5753-4.50380.12073090.10945988100
4.5038-43.8470.15223230.14165993100
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)
10.1380.1415-0.0430.525-0.26960.3073-0.00850.00820.0165-0.07990.02490.02460.0341-0.0260.00010.09290.0002-0.00110.10840.00410.097313.90729.608638.1918
20.19950.2875-0.09050.3472-0.25360.3857-0.03180.03490.0075-0.160.0099-0.098-0.01220.044-0.02510.1379-0.00010.0320.1240.01620.124826.464919.783224.8803
30.09680.135-0.0020.1551-0.05870.18610.00670.0101-0.0447-0.0125-0.0685-0.0823-0.1540.1031-0.0880.1102-0.03050.01810.1480.03280.156431.267725.563939.1147
40.11730.1881-0.09350.2854-0.23860.39930.0369-0.01760.00930.0648-0.0747-0.0437-0.10860.0523-0.02850.1089-0.0213-0.00310.11980.01020.131524.546418.936453.0182
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 333 )A238 - 333
3X-RAY DIFFRACTION3chain 'A' and (resid 334 through 404 )A334 - 404
4X-RAY DIFFRACTION4chain 'A' and (resid 405 through 489 )A405 - 489

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