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

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Basic information

Entry
Database: PDB / ID: 4oal
TitleCrystal structure of maize cytokinin oxidase/dehydrogenase 4 (ZmCKO4) in complex with phenylurea inhibitor CPPU in alternative spacegroup
ComponentsCytokinin dehydrogenase 4
KeywordsOXIDOREDUCTASE / FLAVOPROTEIN / CYTOKININ OXIDASE/DEHYDROGENASE / PHENYL-UREA INHIBITOR
Function / homology
Function and homology information


cytokinin dehydrogenase / cytokinin dehydrogenase activity / cytokinin metabolic process / FAD binding
Similarity search - Function
Cytokinin dehydrogenase 1, FAD/cytokinin binding domain / Cytokinin dehydrogenase 1, FAD and cytokinin binding / : / FAD-linked oxidases, C-terminal domain / Oxygen oxidoreductase covalent FAD-binding site / Oxygen oxidoreductases covalent FAD-binding site. / Cytokinin dehydrogenase, C-terminal domain superfamily / Vanillyl-alcohol Oxidase; Chain A, domain 3 / FAD-linked oxidase-like, C-terminal / 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 / Oxygen oxidoreductase covalent FAD-binding site / Oxygen oxidoreductases covalent FAD-binding site. / Cytokinin dehydrogenase, C-terminal domain superfamily / Vanillyl-alcohol Oxidase; Chain A, domain 3 / FAD-linked oxidase-like, C-terminal / 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 / cytokinin dehydrogenase
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 5, 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 1.3Apr 20, 2016Group: Database references
Revision 1.4Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytokinin dehydrogenase 4
B: Cytokinin dehydrogenase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,25014
Polymers112,5592
Non-polymers2,69212
Water8,863492
1
A: Cytokinin dehydrogenase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5476
Polymers56,2791
Non-polymers1,2685
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cytokinin dehydrogenase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7038
Polymers56,2791
Non-polymers1,4247
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)112.660, 112.620, 203.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Cytokinin dehydrogenase 4


Mass: 56279.270 Da / Num. of mol.: 2 / Fragment: UNP residues 22-541
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: CKX4, CKX4 (CKO4) / Plasmid: pTYB12 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 STAR (DE3) / References: UniProt: E3T1W8, cytokinin dehydrogenase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-245 / 1-(2-chloropyridin-4-yl)-3-phenylurea


Mass: 247.680 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H10ClN3O
#4: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 492 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.77 Å3/Da / Density % sol: 55.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0,1M HEPES pH 7,5, 50% MPD, cocrystallized with 3mM CPPU in DMSO and 5% glycerol , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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: 1.9→27.3 Å / Num. all: 101793 / Num. obs: 101537 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 38 Å2 / Rsym value: 0.13 / Net I/σ(I): 11.44
Reflection shell
Resolution (Å)Mean I/σ(I) obsDiffraction-ID% possible all
1.9-2.011.42198.6
2.01-2.152.581100
2.15-2.324.671100
2.32-2.547.491100
2.54-2.8411.151100
2.84-3.2817.611100
3.28-4.0226.571100
4.02-5.6633.171100
5.66-27.334.66199.6

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
BUSTER2.10.0refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4O95

4o95


Resolution: 1.9→27.25 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.9336 / SU R Cruickshank DPI: 0.128 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2178 5071 5 %RANDOM
Rwork0.2073 ---
obs0.2078 101421 99.99 %-
all-101793 --
Displacement parametersBiso mean: 38.58 Å2
Baniso -1Baniso -2Baniso -3
1--6.1555 Å20 Å20 Å2
2---3.4851 Å20 Å2
3---9.6405 Å2
Refine analyzeLuzzati coordinate error obs: 0.315 Å
Refinement stepCycle: LAST / Resolution: 1.9→27.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6850 0 172 492 7514
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.017213HARMONIC2
X-RAY DIFFRACTIONt_angle_deg19796HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2370SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes142HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1162HARMONIC5
X-RAY DIFFRACTIONt_it7213HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.42
X-RAY DIFFRACTIONt_other_torsion16.1
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion866SEMIHARMONIC5
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_contact8527SEMIHARMONIC4
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4105 371 5 %
Rwork0.3764 7045 -
all0.3782 7416 -
obs--99.99 %
Refinement TLS params.Method: refined / Origin x: -38.3433 Å / Origin y: -27.5956 Å / Origin z: 5.8458 Å
111213212223313233
T-0.0292 Å20.0187 Å2-0.0079 Å2--0.1615 Å20.0472 Å2--0.0091 Å2
L0.154 °20.0602 °2-0.0679 °2-0.0996 °20.238 °2--0.9362 °2
S0.0161 Å °0.0028 Å °-0.0053 Å °-0.0175 Å °0.0002 Å °0.0277 Å °-0.0453 Å °-0.0148 Å °-0.0162 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|40 - A|531 A|601 - A|602 A|603 - A|605 A|701 - A|944 B|603 - B|607 B|701 - B|948 B|40 - B|531 B|601 - B|602 }A40 - 531
2X-RAY DIFFRACTION1{ A|40 - A|531 A|601 - A|602 A|603 - A|605 A|701 - A|944 B|603 - B|607 B|701 - B|948 B|40 - B|531 B|601 - B|602 }A601 - 602
3X-RAY DIFFRACTION1{ A|40 - A|531 A|601 - A|602 A|603 - A|605 A|701 - A|944 B|603 - B|607 B|701 - B|948 B|40 - B|531 B|601 - B|602 }A603 - 605
4X-RAY DIFFRACTION1{ A|40 - A|531 A|601 - A|602 A|603 - A|605 A|701 - A|944 B|603 - B|607 B|701 - B|948 B|40 - B|531 B|601 - B|602 }A701 - 944
5X-RAY DIFFRACTION1{ A|40 - A|531 A|601 - A|602 A|603 - A|605 A|701 - A|944 B|603 - B|607 B|701 - B|948 B|40 - B|531 B|601 - B|602 }B603 - 607
6X-RAY DIFFRACTION1{ A|40 - A|531 A|601 - A|602 A|603 - A|605 A|701 - A|944 B|603 - B|607 B|701 - B|948 B|40 - B|531 B|601 - B|602 }B701 - 948
7X-RAY DIFFRACTION1{ A|40 - A|531 A|601 - A|602 A|603 - A|605 A|701 - A|944 B|603 - B|607 B|701 - B|948 B|40 - B|531 B|601 - B|602 }B40 - 531
8X-RAY DIFFRACTION1{ A|40 - A|531 A|601 - A|602 A|603 - A|605 A|701 - A|944 B|603 - B|607 B|701 - B|948 B|40 - B|531 B|601 - B|602 }B601 - 602

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