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- PDB-3s1d: Glu381Ser mutant of maize cytokinin oxidase/dehydrogenase complex... -

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Basic information

Entry
Database: PDB / ID: 3s1d
TitleGlu381Ser mutant of maize cytokinin oxidase/dehydrogenase complexed with N6-isopentenyladenosine
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 / 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
FLAVIN-ADENINE DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / N-(3-methylbut-2-en-1-yl)adenosine / Cytokinin dehydrogenase 1
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 1.4Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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 1.5Sep 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
Revision 1.6Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)57,66612
Polymers55,3151
Non-polymers2,35111
Water7,062392
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)251.030, 50.400, 51.400
Angle α, β, γ (deg.)90.00, 93.87, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein / Sugars , 2 types, 4 molecules A

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


Mass: 55315.148 Da / Num. of mol.: 1 / Mutation: E381S
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
#6: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
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, 400 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-ZIR / N-(3-methylbut-2-en-1-yl)adenosine


Mass: 335.358 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H21N5O4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 18.015 Da / Num. of mol.: 392 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsSEQUENCE CONFLICT IN UNP ENTRY Q9T0N8 AT THESE POSITIONS

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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: 2.93 Å3/Da / Density % sol: 58.05 %
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: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 9, 2009
RadiationMonochromator: not known / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. all: 65377 / Num. obs: 64966 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Biso Wilson estimate: 26.03 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 15.8
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
1.75-1.790.5052.794629195.9
1.79-1.840.3943.734662199.9
1.84-1.890.3384.384516199.8
1.89-1.950.2635.64419199.5
1.95-2.020.1897.374269199.8
2.02-2.090.1548.884123199.7
2.09-2.170.11910.964018199.7
2.17-2.260.09612.83873199.7
2.26-2.360.08214.93657199.9
2.36-2.470.06717.653545199.9
2.47-2.60.05719.833377199.9
2.6-2.760.0522.493211199.8
2.76-2.950.04424.4729931100
2.95-3.190.03828.012797199.9
3.19-3.490.03331.412585199.8
3.49-3.910.0334.582350199.5
3.91-4.510.02836.492078199.7
4.51-5.520.02637.421760199.8
5.52-7.810.02537.121376199.7
7.81-500.02436.39728190.5

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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: 1.75→25.62 Å / Cor.coef. Fo:Fc: 0.9469 / Cor.coef. Fo:Fc free: 0.9292 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2456 3288 5.07 %RANDOM
Rwork0.2147 ---
all0.2162 65377 --
obs0.2162 64810 --
Displacement parametersBiso mean: 30.84 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å2-0.1829 Å2
2---0.0214 Å20 Å2
3---0.0514 Å2
Refine analyzeLuzzati coordinate error obs: 0.272 Å
Refinement stepCycle: LAST / Resolution: 1.75→25.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3793 0 156 392 4341
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014044HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.025519HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1314SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes106HARMONIC2
X-RAY DIFFRACTIONt_gen_planes626HARMONIC5
X-RAY DIFFRACTIONt_it4044HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.1
X-RAY DIFFRACTIONt_other_torsion15.85
X-RAY DIFFRACTIONt_improper_torsion9HARMONIC0
X-RAY DIFFRACTIONt_chiral_improper_torsion519SEMIHARMONIC5
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_contact4835SEMIHARMONIC4
LS refinement shellResolution: 1.75→1.79 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2893 235 4.92 %
Rwork0.2731 4543 -
all0.2739 4778 -

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