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- PDB-8ckt: Crystal structure of maize cytokinin oxidase/dehydrogenase 4 (CKO... -

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Basic information

Entry
Database: PDB / ID: 8ckt
TitleCrystal structure of maize cytokinin oxidase/dehydrogenase 4 (CKO/CKX4) in complex with inhibitor 2-[(3,5-dichlorophenyl)carbamoylamino]-4-(trifluoromethoxy)benzamide
ComponentsCytokinin dehydrogenase 4
KeywordsFLAVOPROTEIN / Hormone degradation / plant / inhibitor complex
Function / homology
Function and homology information


cytokinin dehydrogenase / cytokinin dehydrogenase activity / cytokinin metabolic process / FAD binding / extracellular region
Similarity search - Function
Cytokinin dehydrogenase 1, FAD/cytokinin binding domain / Cytokinin dehydrogenase 1, FAD and cytokinin binding / : / Cytokinin dehydrogenase, C-terminal domain superfamily / Oxygen oxidoreductase covalent FAD-binding site / Oxygen oxidoreductases covalent FAD-binding site. / FAD-linked oxidase-like, C-terminal / FAD linked oxidase, N-terminal / FAD binding domain / FAD-binding, type PCMH, subdomain 1 ...Cytokinin dehydrogenase 1, FAD/cytokinin binding domain / Cytokinin dehydrogenase 1, FAD and cytokinin binding / : / Cytokinin dehydrogenase, C-terminal domain superfamily / Oxygen oxidoreductase covalent FAD-binding site / Oxygen oxidoreductases covalent FAD-binding site. / FAD-linked oxidase-like, C-terminal / 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
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / : / cytokinin dehydrogenase
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKopecny, D. / Briozzo, P. / Morera, S.
Funding support Czech Republic, 2items
OrganizationGrant numberCountry
Czech Science Foundation21-07661S Czech Republic
Ministry of Education, Youth and Sports of the Czech RepublicCZ.02.1.01/0.0/0.0/16_019/0000827 Czech Republic
CitationJournal: J.Exp.Bot. / Year: 2024
Title: Cytokinin oxidase/dehydrogenase inhibitors: progress towards agricultural practice.
Authors: Nisler, J. / Klimes, P. / Koncitikova, R. / Kadlecova, A. / Voller, J. / Chalaki, M. / Karampelias, M. / Murvanidze, N. / Werbrouck, S.P.O. / Kopecny, D. / Havlicek, L. / De Diego, N. / ...Authors: Nisler, J. / Klimes, P. / Koncitikova, R. / Kadlecova, A. / Voller, J. / Chalaki, M. / Karampelias, M. / Murvanidze, N. / Werbrouck, S.P.O. / Kopecny, D. / Havlicek, L. / De Diego, N. / Briozzo, P. / Morera, S. / Zalabak, D. / Spichal, L.
History
DepositionFeb 16, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _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 1.2Sep 4, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytokinin dehydrogenase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3913
Polymers58,1981
Non-polymers1,1942
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-8 kcal/mol
Surface area18490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.250, 79.250, 204.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Cytokinin dehydrogenase 4


Mass: 58197.684 Da / Num. of mol.: 1 / Mutation: none
Source method: isolated from a genetically manipulated source
Details: ZmCKO4/ZmCKX4 / Source: (gene. exp.) Zea mays (maize) / Gene: CKX4 / Production host: Escherichia coli (E. coli) / References: UniProt: E3T1W8, cytokinin dehydrogenase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-V2F / 2-[[3,5-bis(chloranyl)phenyl]carbamoylamino]-4-(trifluoromethyloxy)benzamide / 2-[(3,5-dichlorophenyl)carbamoylamino]-4-(trifluoromethoxy)benzamide


Mass: 408.159 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H10Cl2F3N3O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 3.23 Å3/Da / Density % sol: 61.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES pH 7.5, 22% MPD, 1 mM inhibitor, and protein at 10 mg ml-1 concentration in the starting drop.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980113 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980113 Å / Relative weight: 1
ReflectionResolution: 2→49.1 Å / Num. obs: 44973 / % possible obs: 100 % / Redundancy: 26.7 % / Biso Wilson estimate: 42.57 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.041 / Rrim(I) all: 0.213 / Rsym value: 0.208 / Net I/σ(I): 16.1
Reflection shellResolution: 2→2.12 Å / Redundancy: 27.1 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 7132 / CC1/2: 0.719 / Rpim(I) all: 0.614 / Rrim(I) all: 3.238 / Rsym value: 3.411 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSBUILT=20220220data reduction
XDSBUILT=20220220data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→43.27 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.904 / SU R Cruickshank DPI: 0.141 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.145 / SU Rfree Blow DPI: 0.138 / SU Rfree Cruickshank DPI: 0.136
RfactorNum. reflection% reflectionSelection details
Rfree0.234 2248 5 %RANDOM
Rwork0.197 ---
obs0.199 44939 99.9 %-
Displacement parametersBiso mean: 48.68 Å2
Baniso -1Baniso -2Baniso -3
1--6.9963 Å20 Å20 Å2
2---6.9963 Å20 Å2
3---13.9926 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: 1 / Resolution: 2→43.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3515 0 79 206 3800
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013700HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.985029HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1223SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes683HARMONIC5
X-RAY DIFFRACTIONt_it3700HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.51
X-RAY DIFFRACTIONt_other_torsion16.38
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion443SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4272SEMIHARMONIC4
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2883 162 5.02 %
Rwork0.2729 3067 -
all0.2737 3229 -
obs--99.17 %

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