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- PDB-5hhz: Crystal structure of maize cytokinin oxidase/dehydrogenase 4 (ZmC... -

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Basic information

Entry
Database: PDB / ID: 5hhz
TitleCrystal structure of maize cytokinin oxidase/dehydrogenase 4 (ZmCKO4) in complex with 6-(3-methylpyrrol-1-yl)-9H-purine
ComponentsCytokinin dehydrogenase 4
KeywordsOXIDOREDUCTASE / flavoenzyme / plant hormone degradation / oxidase/dehydrogenase / Rossmann fold
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
FLAVIN-ADENINE DINUCLEOTIDE / 6-(3-methyl-1H-pyrrol-1-yl)-9H-purine / cytokinin dehydrogenase
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKopecny, D. / Briozzo, P.
CitationJournal: Plant Sci. / Year: 2016
Title: Cytokinin metabolism in maize: Novel evidence of cytokinin abundance, interconversions and formation of a new trans-zeatin metabolic product with a weak anticytokinin activity.
Authors: Hluska, T. / Dobrev, P.I. / Tarkowska, D. / Frebortova, J. / Zalabak, D. / Kopecny, D. / Plihal, O. / Kokas, F. / Briozzo, P. / Zatloukal, M. / Motyka, V. / Galuszka, P.
History
DepositionJan 11, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 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 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2643
Polymers56,2791
Non-polymers9852
Water3,513195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-9 kcal/mol
Surface area18720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.066, 80.066, 203.213
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-875-

HOH

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Components

#1: Protein Cytokinin dehydrogenase 4 / / Cytokinin oxidase/dehydrogenase 4


Mass: 56279.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: CKX4 / Plasmid: PTYB12 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: E3T1W8, cytokinin dehydrogenase
#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-ZME / 6-(3-methyl-1H-pyrrol-1-yl)-9H-purine


Mass: 199.212 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H9N5
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 195 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.89 Å3/Da / Density % sol: 57.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES pH 7,5, 50% MPD, infiltrated for 1h with 2 mM 6-(3-methylpyrrol-1-yl)-9H-purine (MPP) in DMSO and 5% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 27, 2015
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2→49.46 Å / Num. all: 45752 / Num. obs: 44421 / % possible obs: 97.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.35 % / Biso Wilson estimate: 39.54 Å2 / Rsym value: 0.048 / Net I/σ(I): 22.58 / Num. measured all: 326446
Reflection shellResolution: 2→2.12 Å / Redundancy: 7.07 % / Mean I/σ(I) obs: 2.94 / Num. unique all: 7038 / % possible all: 97.1

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
Coot0.8.2model building
XDSJun 17, 2015data reduction
DNAdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4O95

4o95


Resolution: 2→40 Å / Cor.coef. Fo:Fc: 0.9386 / Cor.coef. Fo:Fc free: 0.9355 / SU R Cruickshank DPI: 0.143 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.146 / SU Rfree Blow DPI: 0.127 / SU Rfree Cruickshank DPI: 0.126
RfactorNum. reflection% reflectionSelection details
Rfree0.213 2187 4.93 %RANDOM
Rwork0.1969 ---
obs0.1977 44398 97.29 %-
Displacement parametersBiso mean: 44.91 Å2
Baniso -1Baniso -2Baniso -3
1--6.2636 Å20 Å20 Å2
2---6.2636 Å20 Å2
3---12.5272 Å2
Refine analyzeLuzzati coordinate error obs: 0.242 Å
Refinement stepCycle: LAST / Resolution: 2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3532 0 68 195 3795
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013698HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.995026HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1227SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes72HARMONIC2
X-RAY DIFFRACTIONt_gen_planes597HARMONIC5
X-RAY DIFFRACTIONt_it3698HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.45
X-RAY DIFFRACTIONt_other_torsion16.93
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion446SEMIHARMONIC5
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_contact4195SEMIHARMONIC4
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2799 167 5.16 %
Rwork0.2464 3071 -
all0.2481 3238 -
obs--97.29 %

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