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- PDB-3ebl: Crystal Structure of Rice GID1 complexed with GA4 -

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Basic information

Entry
Database: PDB / ID: 3ebl
TitleCrystal Structure of Rice GID1 complexed with GA4
ComponentsGibberellin receptor GID1
KeywordsHYDROLASE RECEPTOR / alpha/beta hydrolase / lipase / Gibberellin signaling pathway / Hydrolase / Nucleus / Receptor
Function / homology
Function and homology information


raffinose family oligosaccharide biosynthetic process / positive regulation of gibberellic acid mediated signaling pathway / floral organ morphogenesis / gibberellin binding / response to gibberellin / gibberellic acid mediated signaling pathway / Hydrolases / hydrolase activity / nucleus / cytoplasm
Similarity search - Function
Lipase, GDXG, putative serine active site / Lipolytic enzymes "G-D-X-G" family, putative serine active site. / Lipase, GDXG, putative histidine active site / Lipolytic enzymes "G-D-X-G" family, putative histidine active site. / Alpha/beta hydrolase fold-3 / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GIBBERELLIN A4 / NITRATE ION / PHOSPHATE ION / Gibberellin receptor GID1
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsShimada, A. / Nakatsu, T. / Ueguchi-Tanaka, M. / Kato, H. / Matsuoka, M.
CitationJournal: Nature / Year: 2008
Title: Structural basis for gibberellin recognition by its receptor GID1.
Authors: Shimada, A. / Ueguchi-Tanaka, M. / Nakatsu, T. / Nakajima, M. / Naoe, Y. / Ohmiya, H. / Kato, H. / Matsuoka, M.
History
DepositionAug 28, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Mar 26, 2014Group: Database references
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software
Revision 1.4Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gibberellin receptor GID1
B: Gibberellin receptor GID1
C: Gibberellin receptor GID1
D: Gibberellin receptor GID1
E: Gibberellin receptor GID1
F: Gibberellin receptor GID1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)249,41438
Polymers245,4046
Non-polymers4,00932
Water20,4111133
1
A: Gibberellin receptor GID1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5997
Polymers40,9011
Non-polymers6996
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Gibberellin receptor GID1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6327
Polymers40,9011
Non-polymers7326
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Gibberellin receptor GID1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5997
Polymers40,9011
Non-polymers6996
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Gibberellin receptor GID1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5376
Polymers40,9011
Non-polymers6375
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Gibberellin receptor GID1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5085
Polymers40,9011
Non-polymers6084
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Gibberellin receptor GID1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5376
Polymers40,9011
Non-polymers6375
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
E: Gibberellin receptor GID1
F: Gibberellin receptor GID1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,04611
Polymers81,8012
Non-polymers1,2449
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint-50 kcal/mol
Surface area22770 Å2
MethodPISA, PQS
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A: Gibberellin receptor GID1
B: Gibberellin receptor GID1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,23214
Polymers81,8012
Non-polymers1,43012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5740 Å2
ΔGint-45 kcal/mol
Surface area23950 Å2
MethodPISA, PQS
9
C: Gibberellin receptor GID1
D: Gibberellin receptor GID1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,13713
Polymers81,8012
Non-polymers1,33511
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5550 Å2
ΔGint-35 kcal/mol
Surface area22800 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)82.760, 133.895, 118.886
Angle α, β, γ (deg.)90.00, 104.95, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Gibberellin receptor GID1 / Gibberellin-insensitive dwarf protein 1 / Protein GIBBERELLIN INSENSITIVE DWARF1


Mass: 40900.699 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice)
Gene: GID1, Os05g0407500, LOC_Os05g33730, OJ1657_H11.10, P0040B10.6
Plasmid: pET11b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(de3)plys / References: UniProt: Q6L545, Hydrolases

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Non-polymers , 5 types, 1165 molecules

#2: Chemical
ChemComp-GA4 / GIBBERELLIN A4 / Gibberellin


Mass: 332.391 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C19H24O5 / Comment: hormone*YM
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical
ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: NO3
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1133 / Source method: isolated from a natural source / Formula: H2O

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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: 2.59 Å3/Da / Density % sol: 52.57 % / Mosaicity: 0.286 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 15% PEG4000, 8% MPD, 0.2M NaNO3, 0.1M HEPES pH7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ASDC QUANTUM 210 / Detector: CCD / Date: Jun 18, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 193933 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.054 / Χ2: 0.852 / Net I/σ(I): 21.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.973.40.597182310.828192.8
1.97-2.053.50.388189920.812197.5
2.05-2.143.50.284194220.837199.2
2.14-2.253.60.202194670.805199.4
2.25-2.393.60.148195370.856199.7
2.39-2.583.70.106195910.856199.8
2.58-2.843.70.072195920.824199.9
2.84-3.253.80.046196260.8491100
3.25-4.093.80.031196740.892199.9
4.09-503.70.026198010.944199.6

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.936 / WRfactor Rfree: 0.235 / WRfactor Rwork: 0.193 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.809 / SU B: 3.718 / SU ML: 0.108 / SU R Cruickshank DPI: 0.141 / SU Rfree: 0.139 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.142 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24369 9761 5 %RANDOM
Rwork0.20044 ---
obs0.2026 183960 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 84.44 Å2 / Biso mean: 34.444 Å2 / Biso min: 13.99 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å2-2.53 Å2
2--0.36 Å20 Å2
3----1.6 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14549 0 274 1133 15956
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02115244
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5071.95820780
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.00651861
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.68222.656719
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.117152222
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.97315126
X-RAY DIFFRACTIONr_chiral_restr0.0960.22262
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211855
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.20.27195
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.210336
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.21241
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1290.232
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0820.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9281.59551
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.569214912
X-RAY DIFFRACTIONr_scbond_it2.21136437
X-RAY DIFFRACTIONr_scangle_it3.1884.55868
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 662 -
Rwork0.278 12485 -
all-13147 -
obs--100 %

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