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- PDB-3s1e: Pro427Gln mutant of maize cytokinin oxidase/dehydrogenase complex... -

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Basic information

Entry
Database: PDB / ID: 3s1e
TitlePro427Gln mutant of maize cytokinin oxidase/dehydrogenase complexed with N6-isopentenyladenine
ComponentsCytokinin dehydrogenase 1
KeywordsOXIDOREDUCTASE / FAD BINDING PROTEIN / FLAVOPROTEIN / CYTOKININ OXIDASE/DEHYDROGENASE / CYTOKININ BINDING / GLYCOSYLATION / COVALENT FLAVINATION
Function / homology
Function and homology information


cytokinin dehydrogenase / cytokinin dehydrogenase activity / cytokinin metabolic process / FAD binding / oxidoreductase activity / 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 / DI(HYDROXYETHYL)ETHER / N-(3-METHYLBUT-2-EN-1-YL)-9H-PURIN-6-AMINE / Cytokinin dehydrogenase 1
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKopecny, D. / Briozzo, P. / Morera, S.
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
DepositionMay 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2015Group: Database references
Revision 1.2Dec 23, 2015Group: Database references
Revision 1.3Apr 20, 2016Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,62610
Polymers55,3881
Non-polymers2,2389
Water5,603311
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)250.120, 50.110, 51.170
Angle α, β, γ (deg.)90.00, 93.47, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cytokinin dehydrogenase 1 / / Cytokinin oxidase 1 / CKO 1 / COX 1 / ZmCKX1


Mass: 55388.199 Da / Num. of mol.: 1 / Mutation: P427Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Strain: cultivar Nobilis / Gene: CKX1 / Plasmid: pINA6703 / Production host: Yarrowia lipolytica (yeast) / Strain (production host): Po1g / References: UniProt: Q9T0N8, cytokinin dehydrogenase

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Sugars , 2 types, 3 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 317 molecules

#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-ZIP / N-(3-METHYLBUT-2-EN-1-YL)-9H-PURIN-6-AMINE / ISOPENTENYLADENINE


Mass: 203.244 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 311 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsSEQUENCE CONFLICT IN UNP ENTRY Q9T0N8 AT THESE POSITIONS. THE AUTHORS SEQUENCE REFER TO GENE BANK ...SEQUENCE CONFLICT IN UNP ENTRY Q9T0N8 AT THESE POSITIONS. THE AUTHORS SEQUENCE REFER TO GENE BANK NUMBER Y18377.

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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: 2.89 Å3/Da / Density % sol: 57.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 30% (w/v) PEG 1500, 0.5% (w/v)n-octyl beta-D-glucoside, 0.1 M Tris-HCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979629 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 11, 2008
RadiationMonochromator: not known / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979629 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 50263 / Num. obs: 48499 / % possible obs: 96.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Biso Wilson estimate: 27.75 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.66
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
1.9-2.150.3634.1714792195.7
2.15-2.450.1598.8510787196.5
2.45-2.680.09613.695321196.8
2.68-30.06618.65004197.1
3-3.460.04226.874321197.2
3.46-4.230.03336.253718197.3
4.23-60.02840.132936197.6
6-500.02641.791620195.7

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Processing

Software
NameVersionClassification
DNAdata collection
MOLREPphasing
BUSTER2.8.0refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3BW7

3bw7


Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.9493 / Cor.coef. Fo:Fc free: 0.9328 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2311 2472 5.1 %RANDOM
Rwork0.1979 ---
all0.1995 50263 --
obs0.1995 48488 --
Displacement parametersBiso mean: 33.74 Å2
Baniso -1Baniso -2Baniso -3
1-0.7112 Å20 Å20.3447 Å2
2---1.4038 Å20 Å2
3---0.6926 Å2
Refine analyzeLuzzati coordinate error obs: 0.252 Å
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3809 0 148 311 4268
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014105HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.055610HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1356SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes109HARMONIC2
X-RAY DIFFRACTIONt_gen_planes646HARMONIC5
X-RAY DIFFRACTIONt_it4105HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.22
X-RAY DIFFRACTIONt_other_torsion16.65
X-RAY DIFFRACTIONt_improper_torsion9HARMONIC0
X-RAY DIFFRACTIONt_chiral_improper_torsion526SEMIHARMONIC5
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_contact4944SEMIHARMONIC4
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3006 204 5.85 %
Rwork0.2606 3283 -
all0.2628 3487 -

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