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- PDB-6ku3: Crystal structure of gibberellin 2-oxidase3 (GA2ox3)in rice -

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Basic information

Entry
Database: PDB / ID: 6ku3
TitleCrystal structure of gibberellin 2-oxidase3 (GA2ox3)in rice
ComponentsGibberellin 2-beta-dioxygenase 3
KeywordsBIOSYNTHETIC PROTEIN / Jelly Rolls / Metal Ion Binding / Oxygenase
Function / homology
Function and homology information


gibberellin 2beta-dioxygenase / gibberellin catabolic process / gibberellin 2-beta-dioxygenase activity / C-19 gibberellin 2-beta-dioxygenase activity / gibberellin metabolic process / dioxygenase activity / response to light stimulus / metal ion binding
Similarity search - Function
Non-haem dioxygenase N-terminal domain / non-haem dioxygenase in morphine synthesis N-terminal / 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 / GIBBERELLIN A4 / Gibberellin 2-beta-dioxygenase 3
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å
AuthorsTakehara, S. / Mikami, B. / Sakuraba, S. / Matsuoka, M. / Ueguchi-Tanaka, M.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science16H06464 Japan
Japan Society for the Promotion of Science16H06468 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
DepositionAug 30, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 13, 2020Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gibberellin 2-beta-dioxygenase 3
B: Gibberellin 2-beta-dioxygenase 3
C: Gibberellin 2-beta-dioxygenase 3
D: Gibberellin 2-beta-dioxygenase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,53630
Polymers141,4604
Non-polymers4,07626
Water7,242402
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13480 Å2
ΔGint-138 kcal/mol
Surface area48550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.470, 112.739, 149.510
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Gibberellin 2-beta-dioxygenase 3 / Gibberellin 2-beta-hydroxylase 3 / Gibberellin 2-oxidase 3 / OsGA2ox3


Mass: 35365.008 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice)
Gene: GA2OX3, Os01g0757200, LOC_Os01g55240, OJ1414_E05.17 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8S0S6, gibberellin 2beta-dioxygenase

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Non-polymers , 5 types, 428 molecules

#2: Chemical
ChemComp-GA4 / GIBBERELLIN A4


Mass: 332.391 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C19H24O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: hormone*YM
#3: Chemical
ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H6O5
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 402 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.06 Å3/Da / Density % sol: 59.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium sulfate, 0.1 M Tris-HCl (pH 8.5) and 12% (w/v) PEG8000

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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: Oct 31, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 91795 / % possible obs: 99.9 % / Redundancy: 5 % / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.047 / Rrim(I) all: 0.104 / Χ2: 1.326 / Net I/σ(I): 7.8 / Num. measured all: 456613
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.15-2.194.90.61845400.7830.3030.6890.526100
2.19-2.234.90.56545130.8170.2760.630.544100
2.23-2.2750.41545470.8610.2020.4620.5799.9
2.27-2.3250.36645410.9190.1790.4080.57100
2.32-2.3750.3245490.9250.1560.3560.578100
2.37-2.4250.27545450.9440.1340.3060.594100
2.42-2.4850.24545500.9530.120.2740.621100
2.48-2.5550.2245840.9660.1070.2450.622100
2.55-2.625.10.19445630.970.0940.2160.666100
2.62-2.715.10.16745360.9760.0810.1860.727100
2.71-2.815.10.14445540.9830.070.1610.836100
2.81-2.925.10.12745870.9840.0620.1420.922100
2.92-3.055.10.1145900.9870.0530.1221.113100
3.05-3.215.10.09546060.9890.0470.1071.401100
3.21-3.415.10.08446000.9910.0410.0931.727100
3.41-3.6850.07846060.9910.0390.0882.105100
3.68-4.054.90.07646180.9920.0380.0852.79799.9
4.05-4.634.80.0746340.9930.0360.0793.3699.8
4.63-5.834.80.06847110.9930.0350.0773.24499.8
5.83-504.40.06248210.9930.0340.0713.30598

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
Cootmodel building
HKL-2000data reduction
HKL-2000data scaling
HKL-2000data collection
MOLREPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.15→38.8755 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2431 4590 5.01 %
Rwork0.1969 87097 -
obs0.1992 91687 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 207.36 Å2 / Biso mean: 44.209 Å2 / Biso min: 18.13 Å2
Refinement stepCycle: final / Resolution: 2.15→38.8755 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9647 0 274 402 10323
Biso mean--51.65 44.89 -
Num. residues----1262
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1505-2.17490.28161490.26372845299499
2.1749-2.20050.33261680.256128903058100
2.2005-2.22730.31411530.255528302983100
2.2273-2.25550.28951600.247228963056100
2.2555-2.28520.30431660.240128282994100
2.2852-2.31650.29431510.227728823033100
2.3165-2.34960.28381530.228229053058100
2.3496-2.38460.30761380.22228693007100
2.3846-2.42190.29331650.224428643029100
2.4219-2.46160.30981380.220929163054100
2.4616-2.5040.29081270.220328813008100
2.504-2.54950.28751500.223429143064100
2.5495-2.59860.27611520.220428703022100
2.5986-2.65160.30191470.224729013048100
2.6516-2.70920.27171310.223828973028100
2.7092-2.77230.30571460.21928993045100
2.7723-2.84160.24811510.218929013052100
2.8416-2.91840.3051640.223928753039100
2.9184-3.00420.24421440.228529233067100
3.0042-3.10110.2821360.220529053041100
3.1011-3.21190.26441560.216329343090100
3.2119-3.34050.24471630.215128713034100
3.3405-3.49240.26481660.202828953061100
3.4924-3.67640.22621690.193329293098100
3.6764-3.90650.23891820.177428863068100
3.9065-4.20780.21671530.171129253078100
4.2078-4.63070.18251520.146329473099100
4.6307-5.29930.17961580.145829733131100
5.2993-6.67110.19671420.171730153157100
6.6711-38.87550.21921600.1943031319197

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