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- PDB-6yap: Crystal structure of ZmCKO4a in complex with inhibitor 1-(3-Chlor... -

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Basic information

Entry
Database: PDB / ID: 6yap
TitleCrystal structure of ZmCKO4a in complex with inhibitor 1-(3-Chloro-5-trifluoromethoxy-phenyl)-3-[2-(2-hydroxy-ethyl)-phenyl]-urea
ComponentsCytokinin dehydrogenase 4
KeywordsFLAVOPROTEIN / CYTOKININ OXIDASE/DEHYDROGENASE / PHENYL-UREA INHIBITOR / OXIDOREDUCTASE
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 / 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 / Chem-OHZ / cytokinin dehydrogenase
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 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

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Assembly

Deposited unit
A: Cytokinin dehydrogenase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,84110
Polymers58,1981
Non-polymers1,6439
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint8 kcal/mol
Surface area18430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.670, 79.670, 203.700
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cytokinin dehydrogenase 4 /


Mass: 58197.684 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: CKX4 / Production host: Escherichia coli (E. coli) / References: UniProt: E3T1W8, cytokinin dehydrogenase

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Non-polymers , 5 types, 215 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: 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
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.78 Å3/Da / Density % sol: 55.71 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: HEPES, MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.9→27.81 Å / Num. obs: 52720 / % possible obs: 99.9 % / Redundancy: 25.8 % / Biso Wilson estimate: 48.09 Å2 / CC1/2: 1 / Rsym value: 0.07 / Net I/σ(I): 24.6
Reflection shellResolution: 1.9→2.01 Å / Num. unique obs: 8327 / CC1/2: 0.886

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Phasing

PhasingMethod: molecular replacement

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Processing

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

6yao


Resolution: 1.9→27.81 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.938 / SU R Cruickshank DPI: 0.121 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.124 / SU Rfree Blow DPI: 0.114 / SU Rfree Cruickshank DPI: 0.113
RfactorNum. reflection% reflectionSelection details
Rfree0.222 2630 5 %RANDOM
Rwork0.201 ---
obs0.202 52600 99.9 %-
Displacement parametersBiso max: 154.35 Å2 / Biso mean: 55.43 Å2 / Biso min: 32.05 Å2
Baniso -1Baniso -2Baniso -3
1--8.2863 Å20 Å20 Å2
2---8.2863 Å20 Å2
3---16.5725 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: final / Resolution: 1.9→27.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3470 0 106 206 3782
Biso mean--57.07 58.44 -
Num. residues----451
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1205SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes659HARMONIC5
X-RAY DIFFRACTIONt_it3663HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion437SEMIHARMONIC5
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_contact4190SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3663HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4966HARMONIC20.98
X-RAY DIFFRACTIONt_omega_torsion3.46
X-RAY DIFFRACTIONt_other_torsion16.06
LS refinement shellResolution: 1.9→1.95 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3172 189 5 %
Rwork0.3083 3592 -
all0.3088 3781 -
obs--99.63 %

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