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- PDB-4o95: Crystal structure of maize cytokinin oxidase/dehydrogenase 4 (ZmC... -

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Basic information

Entry
Database: PDB / ID: 4o95
TitleCrystal structure of maize cytokinin oxidase/dehydrogenase 4 (ZmCKO4) in complex with phenylurea inhibitor CPPU
ComponentsCytokinin dehydrogenase 4
KeywordsOXIDOREDUCTASE / CYTOKININ / FLAVOPROTEIN / PHENYL-UREA INHIBITOR
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 / FAD-linked oxidases, C-terminal domain / Cytokinin dehydrogenase, C-terminal domain superfamily / Oxygen oxidoreductase covalent FAD-binding site / Oxygen oxidoreductases covalent FAD-binding site. / 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 ...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 / Oxygen oxidoreductase covalent FAD-binding site / Oxygen oxidoreductases covalent FAD-binding site. / 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
1-(2-chloropyridin-4-yl)-3-phenylurea / FLAVIN-ADENINE DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / cytokinin dehydrogenase
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsKopecny, D. / Morera, S. / Vigouroux, A. / Koncitikova, R.
CitationJournal: Febs J. / Year: 2016
Title: Kinetic and structural investigation of the cytokinin oxidase/dehydrogenase active site.
Authors: Kopecny, D. / Koncitikova, R. / Popelka, H. / Briozzo, P. / Vigouroux, A. / Kopecna, M. / Zalabak, D. / Sebela, M. / Skopalova, J. / Frebort, I. / Morera, S.
History
DepositionJan 1, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 1, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2015Group: Database references
Revision 1.2Nov 25, 2015Group: Database references
Revision 1.3Aug 24, 2022Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / struct_conn / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)58,31617
Polymers56,2791
Non-polymers2,03616
Water3,099172
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.450, 74.450, 208.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: 56279.270 Da / Num. of mol.: 1 / Fragment: UNP residues 22-541
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: CKX4 / Plasmid: pTYB12 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 STAR (DE3) / References: UniProt: E3T1W8, cytokinin dehydrogenase

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Non-polymers , 7 types, 188 molecules

#2: 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
#3: Chemical ChemComp-245 / 1-(2-chloropyridin-4-yl)-3-phenylurea / Forchlorfenuron


Mass: 247.680 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H10ClN3O
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 2.48 Å3/Da / Density % sol: 50.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 22% ethylene glycol, co-crystallized with 3mM CPPU in DMSO, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97934 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 8, 2013
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. all: 60144 / Num. obs: 58646 / % possible obs: 97.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 33.15 Å2 / Rsym value: 0.071 / Net I/σ(I): 13.14
Reflection shellResolution: 1.75→1.86 Å / % possible all: 98.9

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
BUSTER2.10.0refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→42.67 Å / Cor.coef. Fo:Fc: 0.9519 / Cor.coef. Fo:Fc free: 0.9403 / SU R Cruickshank DPI: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2071 2931 5 %RANDOM
Rwork0.187 ---
obs0.188 58603 97.52 %-
Displacement parametersBiso mean: 50.85 Å2
Baniso -1Baniso -2Baniso -3
1--5.072 Å20 Å20 Å2
2---5.072 Å20 Å2
3---10.1439 Å2
Refine analyzeLuzzati coordinate error obs: 0.272 Å
Refinement stepCycle: LAST / Resolution: 1.75→42.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3558 0 134 172 3864
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013782HARMONIC2
X-RAY DIFFRACTIONt_angle_deg15111HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1252SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes71HARMONIC2
X-RAY DIFFRACTIONt_gen_planes610HARMONIC5
X-RAY DIFFRACTIONt_it3782HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion3.71
X-RAY DIFFRACTIONt_other_torsion16.18
X-RAY DIFFRACTIONt_chiral_improper_torsion448SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact4439SEMIHARMONIC4
LS refinement shellResolution: 1.75→1.79 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2756 215 5.01 %
Rwork0.237 4077 -
all0.2388 4292 -
obs-4292 97.52 %
Refinement TLS params.Method: refined / Origin x: -27.0376 Å / Origin y: -3.9423 Å / Origin z: -21.5798 Å
111213212223313233
T-0.083 Å2-0.0374 Å2-0.0029 Å2--0.1677 Å20.0117 Å2---0.2388 Å2
L0.5989 °2-0.0676 °20.3927 °2-0.7627 °2-0.5214 °2--3.709 °2
S0.0201 Å °0.0354 Å °-0.0142 Å °0.0847 Å °-0.0712 Å °0.077 Å °0.0395 Å °-0.1654 Å °0.0511 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|38 - A|531 A|601 - A|602 A|603 - A|616 A|701 - A|872 }A38 - 531
2X-RAY DIFFRACTION1{ A|38 - A|531 A|601 - A|602 A|603 - A|616 A|701 - A|872 }A601 - 602
3X-RAY DIFFRACTION1{ A|38 - A|531 A|601 - A|602 A|603 - A|616 A|701 - A|872 }A603 - 616
4X-RAY DIFFRACTION1{ A|38 - A|531 A|601 - A|602 A|603 - A|616 A|701 - A|872 }A701 - 872

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