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- PDB-6kun: Crystal structure of dioxygenase for auxin oxidation (DAO) in rice -

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Basic information

Entry
Database: PDB / ID: 6kun
TitleCrystal structure of dioxygenase for auxin oxidation (DAO) in rice
Components2-oxoglutarate-dependent dioxygenase DAO
KeywordsBIOSYNTHETIC PROTEIN / Jelly Rolls / Metal Ion Binding / Oxygenase
Function / homology
Function and homology information


auxin catabolic process / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor / dioxygenase activity / metal ion binding
Similarity search - Function
: / Non-haem dioxygenase N-terminal domain / non-haem dioxygenase in morphine synthesis N-terminal / Isopenicillin N synthase-like, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily / Isopenicillin N synthase-like superfamily / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile.
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / 1H-INDOL-3-YLACETIC ACID / 2-oxoglutarate-dependent dioxygenase DAO
Similarity search - Component
Biological speciesOryza sativa subsp. indica (long-grained rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.002 Å
AuthorsTakehara, S. / Mikami, B. / Sakuraba, S. / Matsuoka, M. / Ueguchi-Tanaka, M.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)16H06468 Japan
Japan Society for the Promotion of Science (JSPS)16H06464 Japan
CitationJournal: Nat Commun / Year: 2020
Title: A common allosteric mechanism regulates homeostatic inactivation of auxin and gibberellin.
Authors: Takehara, S. / Sakuraba, S. / Mikami, B. / Yoshida, H. / Yoshimura, H. / Itoh, A. / Endo, M. / Watanabe, N. / Nagae, T. / Matsuoka, M. / Ueguchi-Tanaka, M.
History
DepositionSep 2, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: 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
Revision 1.2Oct 23, 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

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Assembly

Deposited unit
A: 2-oxoglutarate-dependent dioxygenase DAO
B: 2-oxoglutarate-dependent dioxygenase DAO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,29410
Polymers64,2832
Non-polymers1,0118
Water5,603311
1
B: 2-oxoglutarate-dependent dioxygenase DAO
hetero molecules

A: 2-oxoglutarate-dependent dioxygenase DAO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,29410
Polymers64,2832
Non-polymers1,0118
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area2980 Å2
ΔGint5 kcal/mol
Surface area25020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.247, 78.304, 94.003
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 2-oxoglutarate-dependent dioxygenase DAO / Protein DIOXYGENASE FOR AUXIN OXIDATION


Mass: 32141.322 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. indica (long-grained rice)
Gene: DAO, OsI_16300, OSIGBa0106G07.8 / Production host: Escherichia coli (E. coli)
References: UniProt: Q01IX6, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor
#2: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H6O5
#3: Chemical ChemComp-IAC / 1H-INDOL-3-YLACETIC ACID / INDOLE ACETIC ACID


Mass: 175.184 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H9NO2 / Feature type: SUBJECT OF INVESTIGATION / Comment: hormone*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.19 Å3/Da / Density % sol: 43.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Sodium acetate, 0.2 M ammonium sulfate and 22% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Apr 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 38070 / % possible obs: 100 % / Redundancy: 9.5 % / Rsym value: 0.054 / Net I/σ(I): 36.2
Reflection shellResolution: 2→2.03 Å / Num. unique obs: 2675 / Rsym value: 0.061

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
Coot3.25model building
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KU3

6ku3


Resolution: 2.002→40.3073 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 31.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2427 1870 4.94 %
Rwork0.1877 36020 -
obs0.1905 37890 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 122.58 Å2 / Biso mean: 35.8703 Å2 / Biso min: 9.85 Å2
Refinement stepCycle: final / Resolution: 2.002→40.3073 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4436 0 74 311 4821
Biso mean--61.82 42.22 -
Num. residues----588
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0021-2.05630.3061610.22232675283698
2.0563-2.11680.27271370.220927292866100
2.1168-2.18510.23641450.20982734287999
2.1851-2.26320.28241470.206227382885100
2.2632-2.35380.26351290.195427652894100
2.3538-2.46090.2671110.203827652876100
2.4609-2.59060.26211430.207427532896100
2.5906-2.75290.27391710.199127362907100
2.7529-2.96540.24031120.190327992911100
2.9654-3.26370.27411630.185427952958100
3.2637-3.73560.2481510.164827922943100
3.7356-4.70540.16981640.14928352999100
4.7054-40.30730.24841360.20652904304098
Refinement TLS params.Method: refined / Origin x: 37.5395 Å / Origin y: -9.0634 Å / Origin z: -24.0334 Å
111213212223313233
T0.1349 Å2-0.0093 Å2-0.0076 Å2-0.0996 Å2-0.0032 Å2--0.1263 Å2
L0.7127 °2-0.2109 °20.0648 °2-0.0055 °2-0.0291 °2--0.0721 °2
S-0.0356 Å °0.0375 Å °-0.0232 Å °-0.0048 Å °0.0134 Å °0.0199 Å °-0.005 Å °-0.0083 Å °-0.0002 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 300
2X-RAY DIFFRACTION1allB3 - 300
3X-RAY DIFFRACTION1allD1 - 292
4X-RAY DIFFRACTION1allD293 - 295
5X-RAY DIFFRACTION1allD296 - 313
6X-RAY DIFFRACTION1allC1 - 2
7X-RAY DIFFRACTION1allE1
8X-RAY DIFFRACTION1allE2
9X-RAY DIFFRACTION1allF2
10X-RAY DIFFRACTION1allF3
11X-RAY DIFFRACTION1allF4 - 6

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