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- PDB-6xma: Crystal structure of iron-bound LSD4 from Sphingobium sp. strain SYK-6 -

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Basic information

Entry
Database: PDB / ID: 6xma
TitleCrystal structure of iron-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 / MOLECULAR REPLACEMENT / 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)55,1263
Polymers54,9741
Non-polymers1522
Water15,763875
1
A: Dioxygenase
hetero molecules

A: Dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,2526
Polymers109,9482
Non-polymers3044
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Unit cell
Length a, b, c (Å)86.030, 112.527, 115.384
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-705-

HOH

21A-1337-

HOH

31A-1446-

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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 875 / 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: 2.54 Å3/Da / Density % sol: 51.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.4 M magnesium acetate and 28% 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: 1.45→50 Å / Num. obs: 190316 / % possible obs: 99.9 % / Redundancy: 16.1 % / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.024 / Rrim(I) all: 0.113 / Χ2: 1.02 / Net I/σ(I): 12.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.45-1.484.20.55847520.8290.2910.6330.73397.3
1.48-1.57.50.53348880.9240.2040.5720.72499.9
1.5-1.5310.60.50349000.9560.1610.5290.777100
1.53-1.5611.30.43449020.9710.1350.4550.747100
1.56-1.611.80.40349400.9760.1220.4210.769100
1.6-1.6312.40.34348760.9820.1010.3580.776100
1.63-1.6712.80.31449080.9860.0910.3270.809100
1.67-1.7213.40.28649150.9880.0810.2970.894100
1.72-1.7713.90.24649160.9920.0690.2560.92100
1.77-1.8314.40.21849380.9940.0590.2261.033100
1.83-1.89150.19249180.9950.0510.1981.189100
1.89-1.9715.60.1549270.9960.0390.1551.254100
1.97-2.0616.20.13249330.9960.0340.1361.304100
2.06-2.1716.80.11249520.9970.0280.1151.158100
2.17-2.3180.12249410.9960.0290.1261.23100
2.3-2.4820.10.12749710.9960.0290.1311.136100
2.48-2.73210.11949560.9970.0260.1221.111100
2.73-3.1222.70.10850190.9970.0230.1111.047100
3.12-3.9428.20.11150350.9980.0210.1131.093100
3.94-5033.90.07252030.9990.0120.0730.90499.8

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Phasing

PhasingMethod: molecular replacement

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Processing

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

6ojr


Resolution: 1.45→29.788 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 17.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1707 9418 5 %
Rwork0.1492 179097 -
obs0.1503 188515 98.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.97 Å2 / Biso mean: 16.9294 Å2 / Biso min: 5.98 Å2
Refinement stepCycle: final / Resolution: 1.45→29.788 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3805 0 6 875 4686
Biso mean--24.27 27.91 -
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 (%)
1.45-1.46610.2722690.2732477380
1.4661-1.48330.26612980.2385574794
1.4833-1.50140.22843220.19786087100
1.5014-1.52040.22653200.18066104100
1.5204-1.54040.2243170.17426045100
1.5404-1.56150.18143050.16576053100
1.5615-1.58380.20482970.17146167100
1.5838-1.60750.20293500.16596013100
1.6075-1.63260.17963140.1656114100
1.6326-1.65930.21443060.16336087100
1.6593-1.6880.18573180.16056058100
1.688-1.71860.2133130.16076081100
1.7186-1.75170.19473210.17516062100
1.7517-1.78750.18722890.1666085100
1.7875-1.82630.23143210.1798604699
1.8263-1.86880.19773300.1786598299
1.8688-1.91550.20413010.163600499
1.9155-1.96730.19663070.1521605399
1.9673-2.02520.15943410.1528600199
2.0252-2.09050.14733140.1393598299
2.0905-2.16520.15223420.143600899
2.1652-2.25190.17493430.1344596499
2.2519-2.35430.16232680.1382598698
2.3543-2.47840.15763150.135592697
2.4784-2.63360.16012760.1403591097
2.6336-2.83680.15923390.1403585197
2.8368-3.1220.15393080.1434590697
3.122-3.57310.15862960.1339599799
3.5731-4.49920.11783340.1197600499
4.4992-29.7880.17193440.1445600199
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)
10.11830.2287-0.14970.3575-0.30490.42930.0434-0.02990.01070.0794-0.0805-0.0458-0.11760.0874-0.04760.0953-0.0293-0.00270.09550.00660.094924.680318.9853.1985
20.09040.1358-0.03360.3834-0.1690.3604-0.00320.01510.0146-0.04530.01620.01750.019-0.00290.02410.0594-0.00230.00140.07280.0030.070413.98749.537138.4772
30.14230.1725-0.0450.145-0.1290.2159-0.05150.10770.0066-0.20190.0397-0.01410.0472-0.0073-0.00750.1505-0.010.02230.11940.0150.113920.615317.904819.5098
40.17080.3149-0.07320.2354-0.20560.3763-0.00080.0065-0.045-0.0378-0.0232-0.0809-0.06850.1022-0.00130.0994-0.01120.02480.11520.02110.115930.431523.576129.3565
50.05090.085-0.06370.0762-0.04310.20280.0014-0.0472-0.05740.0143-0.0686-0.0809-0.19270.0947-0.03380.0865-0.05350.00950.11820.0370.131931.660125.457544.4017
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 405 through 489 )A405 - 489
2X-RAY DIFFRACTION2chain 'A' and (resid 2 through 237 )A2 - 237
3X-RAY DIFFRACTION3chain 'A' and (resid 238 through 277 )A238 - 277
4X-RAY DIFFRACTION4chain 'A' and (resid 278 through 358 )A278 - 358
5X-RAY DIFFRACTION5chain 'A' and (resid 359 through 404 )A359 - 404

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