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- PDB-6c80: Crystal structure of a flax cytokinin oxidase -

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Basic information

Entry
Database: PDB / ID: 6c80
TitleCrystal structure of a flax cytokinin oxidase
Componentscytokinin oxidase LuCKX1.1
KeywordsIMMUNE SYSTEM / Plant immunity / Effector / Cytokinin / Cytokinin oxidase
Function / homology
Function and homology information


cytokinin dehydrogenase / cytokinin dehydrogenase activity / cytokinin metabolic process / FAD binding
Similarity search - Function
Cytokinin dehydrogenase 1, FAD/cytokinin binding domain / Cytokinin dehydrogenase 1, FAD and cytokinin binding / FAD-linked oxidases, C-terminal domain / Cytokinin dehydrogenase, C-terminal domain superfamily / FAD-linked oxidase-like, C-terminal / Vanillyl-alcohol Oxidase; Chain A, domain 3 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 - #10 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 ...Cytokinin dehydrogenase 1, FAD/cytokinin binding domain / Cytokinin dehydrogenase 1, FAD and cytokinin binding / FAD-linked oxidases, C-terminal domain / Cytokinin dehydrogenase, C-terminal domain superfamily / FAD-linked oxidase-like, C-terminal / Vanillyl-alcohol Oxidase; Chain A, domain 3 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 - #10 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 / FAD linked oxidase, N-terminal / FAD binding domain / FAD-binding, type PCMH, subdomain 1 / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / AMMONIUM ION / DI(HYDROXYETHYL)ETHER / Chem-PG6 / Cytokinin dehydrogenase
Similarity search - Component
Biological speciesLinum usitatissimum (flax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsWan, L. / Williams, S. / Kobe, B.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP120100685 Australia
CitationJournal: Mol. Plant Pathol. / Year: 2019
Title: Structural and functional insights into the modulation of the activity of a flax cytokinin oxidase by flax rust effector AvrL567-A.
Authors: Wan, L. / Koeck, M. / Williams, S.J. / Ashton, A.R. / Lawrence, G.J. / Sakakibara, H. / Kojima, M. / Bottcher, C. / Ericsson, D.J. / Hardham, A.R. / Jones, D.A. / Ellis, J.G. / Kobe, B. / Dodds, P.N.
History
DepositionJan 23, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 6, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Jun 5, 2024Group: Data collection / Database references / Category: citation / refln / Item: _citation.country

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: cytokinin oxidase LuCKX1.1
B: cytokinin oxidase LuCKX1.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,96222
Polymers108,6512
Non-polymers3,31120
Water10,431579
1
A: cytokinin oxidase LuCKX1.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8709
Polymers54,3251
Non-polymers1,5448
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: cytokinin oxidase LuCKX1.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,09213
Polymers54,3251
Non-polymers1,76712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.226, 58.929, 188.867
Angle α, β, γ (deg.)90.000, 95.620, 90.000
Int Tables number5
Space group name H-MI121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein cytokinin oxidase LuCKX1.1


Mass: 54325.402 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Linum usitatissimum (flax) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0U1ZL01*PLUS

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Non-polymers , 6 types, 599 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PG6 / 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE


Mass: 266.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O6
#6: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H4N
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 579 / Source method: isolated from a natural source / Formula: H2O

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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: 2.33 Å3/Da / Density % sol: 47.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.24 M tribasic ammonium citrate (pH 8.0) and 18% (w/v) PEG-3350

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953691 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953691 Å / Relative weight: 1
ReflectionResolution: 1.78→85.08 Å / Num. obs: 95714 / % possible obs: 99.8 % / Redundancy: 7.5 % / Biso Wilson estimate: 17.59 Å2 / Net I/σ(I): 2.8
Reflection scaleGroup code: 1
Reflection shellResolution: 1.78→1.88 Å

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2EXR

2exr


Resolution: 1.78→49.355 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.43 / Phase error: 16.85
RfactorNum. reflection% reflection
Rfree0.1837 4795 5.01 %
Rwork0.1507 --
obs0.1523 95697 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 148.26 Å2 / Biso mean: 23.07 Å2 / Biso min: 7.96 Å2
Refinement stepCycle: final / Resolution: 1.78→49.355 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7552 0 228 579 8359
Biso mean--30.66 29.22 -
Num. residues----964
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078030
X-RAY DIFFRACTIONf_angle_d1.15410891
X-RAY DIFFRACTIONf_chiral_restr0.0481147
X-RAY DIFFRACTIONf_plane_restr0.0061387
X-RAY DIFFRACTIONf_dihedral_angle_d14.1282940
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7797-1.79990.31071340.26092737287193
1.7999-1.82110.25371540.209130683222100
1.8211-1.84330.24641580.190230453203100
1.8433-1.86660.24231710.186229773148100
1.8666-1.89120.25441490.172130163165100
1.8912-1.91710.20941680.170530303198100
1.9171-1.94450.20621560.16430473203100
1.9445-1.97350.21641630.158229963159100
1.9735-2.00440.20821440.158830193163100
2.0044-2.03720.21341540.149430213175100
2.0372-2.07240.1951760.146430033179100
2.0724-2.110.21071550.14430343189100
2.11-2.15060.19561550.141830363191100
2.1506-2.19450.18961500.145330383188100
2.1945-2.24220.19061570.148230153172100
2.2422-2.29440.19311560.147830533209100
2.2944-2.35180.18941480.148330613209100
2.3518-2.41540.19161600.146930063166100
2.4154-2.48640.17841780.154930203198100
2.4864-2.56670.18151590.145530493208100
2.5667-2.65840.17961800.151129913171100
2.6584-2.76490.18871700.150630363206100
2.7649-2.89070.19071600.151430343194100
2.8907-3.04310.18411550.151130903245100
3.0431-3.23370.1551580.144330213179100
3.2337-3.48330.16931520.137330893241100
3.4833-3.83370.16311600.136530543214100
3.8337-4.38820.14711670.127730693236100
4.3882-5.52740.15331790.141330783257100
5.5274-49.37440.18171690.171531693338100
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)
11.77082.2544-0.6376.2557-3.77574.5394-0.05360.1817-0.0843-0.3369-0.0929-0.32360.14350.23870.15260.1930.03250.03470.1828-0.0250.1272170.098323.1541381.2584
21.7765-0.33020.73141.6309-0.0862.3423-0.02120.07780.1724-0.17460.0272-0.0618-0.190.09010.01480.1515-0.01370.04080.13610.00630.0869168.261829.2593389.401
30.4217-0.17310.05941.2191-0.4040.7063-0.0243-0.00710.07050.01460.0316-0.1081-0.05650.04-0.00530.0861-0.01980.00680.0986-0.0130.0912170.567723.2438407.2395
43.18961.43270.21564.63841.4412.2679-0.00170.0655-0.19790.23620.0965-0.11620.25570.0822-0.06790.11910.0174-0.00940.10280.04240.0597169.92010.4603413.5215
52.15211.01730.10132.6389-0.98611.66140.0636-0.1661-0.12990.2712-0.1326-0.248-0.06710.1570.07060.11480.019-0.00130.1128-0.00640.1239177.77275.8831419.8443
61.86860.55740.04551.7525-0.24882.30640.07080.2417-0.3661-0.1960.0252-0.07010.13550.0758-0.02350.14080.0057-0.01830.0805-0.03570.1458165.44436.2851401.5632
71.62240.41780.55812.0552-0.66071.34470.04110.1019-0.1347-0.05870.0840.00690.1554-0.0408-0.02540.0869-0.02230.0120.13020.0070.0894158.97289.4292406.2713
81.4152-0.0652-0.20132.5051-0.34811.17580.03570.1125-0.0612-0.18630.03440.38760.0175-0.1799-0.08850.1101-0.0119-0.04180.1731-0.01540.1714150.191120.0115396.1672
91.34580.2142-0.51592.88351.38682.4813-0.03280.18410.0188-0.4533-0.06020.2494-0.1069-0.12830.00450.18430.0183-0.02180.19150.01710.1263210.8618-18.7527381.0609
100.4152-0.3005-0.18280.86280.19120.6914-0.01880.0644-0.0551-0.0084-0.00690.10340.1027-0.03740.03870.1101-0.026-0.00350.1077-0.00650.1053206.8865-20.238401.6546
112.30690.5573-0.02132.39570.60422.11870.007-0.06930.29290.1209-0.05950.2372-0.1608-0.1494-0.01840.12740.02130.00140.1107-0.01120.1531199.14512.0372415.1042
121.56720.3789-0.25132.02390.20071.24490.02160.12330.226-0.09120.0542-0.0994-0.1310.1162-0.04080.1077-0.02310.00140.12450.01640.1424217.399-3.3505404.4319
132.7583-0.8844-0.65043.5630.61154.0671-0.00280.1030.0136-0.00520.1395-0.4450.16160.4-0.13640.1020.0302-0.00810.172-0.00310.1802228.9586-23.8877397.0052
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 44 through 78 )A44 - 78
2X-RAY DIFFRACTION2chain 'A' and (resid 79 through 136 )A79 - 136
3X-RAY DIFFRACTION3chain 'A' and (resid 137 through 270 )A137 - 270
4X-RAY DIFFRACTION4chain 'A' and (resid 271 through 313 )A271 - 313
5X-RAY DIFFRACTION5chain 'A' and (resid 314 through 362 )A314 - 362
6X-RAY DIFFRACTION6chain 'A' and (resid 363 through 400 )A363 - 400
7X-RAY DIFFRACTION7chain 'A' and (resid 401 through 457 )A401 - 457
8X-RAY DIFFRACTION8chain 'A' and (resid 458 through 528 )A458 - 528
9X-RAY DIFFRACTION9chain 'B' and (resid 44 through 78 )B44 - 78
10X-RAY DIFFRACTION10chain 'B' and (resid 79 through 270 )B79 - 270
11X-RAY DIFFRACTION11chain 'B' and (resid 271 through 362 )B271 - 362
12X-RAY DIFFRACTION12chain 'B' and (resid 363 through 488 )B363 - 488
13X-RAY DIFFRACTION13chain 'B' and (resid 489 through 532 )B489 - 532

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