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- PDB-6yaq: Crystal sttructure of ZmCKO8 in complex with inhibitor 1-(3-Chlor... -

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Basic information

Entry
Database: PDB / ID: 6yaq
TitleCrystal sttructure of ZmCKO8 in complex with inhibitor 1-(3-Chloro-5-trifluoromethoxy-phenyl)-3-[2-(2-hydroxy-ethyl)-phenyl]-urea
ComponentsCytokinin dehydrogenase 8
KeywordsFLAVOPROTEIN / CYTOKININ OXIDASE/DEHYDROGENASE / PHENYL-UREA INHIBITOR
Function / homology
Function and homology information


cytokinin dehydrogenase / cytokinin dehydrogenase activity / cytokinin metabolic process / FAD binding / oxidoreductase activity / extracellular space / 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 / FAD-binding domain, PCMH-type ...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 / ISOPROPYL ALCOHOL / Chem-OHZ / DI(HYDROXYETHYL)ETHER / cytokinin dehydrogenase / Cytokinin dehydrogenase
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsKopecny, D. / Briozzo, P. / Morera, S.
CitationJournal: J.Exp.Bot. / Year: 2021
Title: Diphenylurea-derived cytokinin oxidase/dehydrogenase inhibitors for biotechnology and agriculture.
Authors: Nisler, J. / Kopecny, D. / Pekna, Z. / Koncitikova, R. / Koprna, R. / Murvanidze, N. / Werbrouck, S.P.O. / Havlicek, L. / De Diego, N. / Kopecna, M. / Wimmer, Z. / Briozzo, P. / Morera, S. / ...Authors: Nisler, J. / Kopecny, D. / Pekna, Z. / Koncitikova, R. / Koprna, R. / Murvanidze, N. / Werbrouck, S.P.O. / Havlicek, L. / De Diego, N. / Kopecna, M. / Wimmer, Z. / Briozzo, P. / Morera, S. / Zalabak, D. / Spichal, L. / Strnad, M.
History
DepositionMar 12, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Jan 24, 2024Group: 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: Cytokinin dehydrogenase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,24620
Polymers56,9061
Non-polymers2,34019
Water7,566420
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint41 kcal/mol
Surface area20050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.518, 101.518, 128.171
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cytokinin dehydrogenase 8


Mass: 56906.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: CKX8 / Production host: Escherichia coli (E. coli)
References: UniProt: E3T1X2, UniProt: A0A1D6QQD6*PLUS, cytokinin dehydrogenase

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Non-polymers , 6 types, 439 molecules

#2: Chemical ChemComp-OHZ / 1-(3-Chloro-5-trifluoromethoxy-phenyl)-3-[2-(2-hydroxy-ethyl)-phenyl]-urea / 1-[3-chloranyl-5-(trifluoromethyloxy)phenyl]-3-[2-(2-hydroxyethyl)phenyl]urea


Mass: 374.742 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H14ClF3N2O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 420 / 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: 3.35 Å3/Da / Density % sol: 63.29 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: HEPES, PEG 4K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.95→47.2 Å / Num. obs: 54431 / % possible obs: 99.9 % / Redundancy: 20 % / CC1/2: 0.998 / Rsym value: 0.163 / Net I/σ(I): 13
Reflection shellResolution: 1.95→2.05 Å / Num. unique obs: 7754 / CC1/2: 0.558

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YAO

6yao


Resolution: 1.95→39 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.937 / SU R Cruickshank DPI: 0.124 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.128 / SU Rfree Blow DPI: 0.119 / SU Rfree Cruickshank DPI: 0.117
RfactorNum. reflection% reflectionSelection details
Rfree0.21 2721 5 %RANDOM
Rwork0.182 ---
obs0.184 54427 99.9 %-
Displacement parametersBiso max: 114.11 Å2 / Biso mean: 33.19 Å2 / Biso min: 15.2 Å2
Baniso -1Baniso -2Baniso -3
1--3.3282 Å20 Å20 Å2
2---3.3282 Å20 Å2
3---6.6565 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: final / Resolution: 1.95→39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3869 0 155 420 4444
Biso mean--45 41.68 -
Num. residues----499
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1412SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes756HARMONIC5
X-RAY DIFFRACTIONt_it4159HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion516SEMIHARMONIC5
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_contact5016SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4159HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg5640HARMONIC20.97
X-RAY DIFFRACTIONt_omega_torsion3.52
X-RAY DIFFRACTIONt_other_torsion15.64
LS refinement shellResolution: 1.95→2 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 201 5.01 %
Rwork0.3271 3809 -
all0.3286 4010 -
obs--99.75 %

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