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- PDB-3ed1: Crystal Structure of Rice GID1 complexed with GA3 -

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Basic information

Entry
Database: PDB / ID: 3ed1
TitleCrystal Structure of Rice GID1 complexed with GA3
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 histidine active site / Lipolytic enzymes "G-D-X-G" family, putative histidine active site. / Lipase, GDXG, putative serine active site / Lipolytic enzymes "G-D-X-G" family, putative serine active site. / Alpha/beta hydrolase fold-3 / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold ...: / Lipase, GDXG, putative histidine active site / Lipolytic enzymes "G-D-X-G" family, putative histidine active site. / Lipase, GDXG, putative serine active site / Lipolytic enzymes "G-D-X-G" family, putative serine 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 A3 / NITRATE ION / PHOSPHATE ION / Gibberellin receptor GID1
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 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
DepositionSep 2, 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 1.4Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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)249,12532
Polymers245,4046
Non-polymers3,72126
Water19,9251106
1
A: Gibberellin receptor GID1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5516
Polymers40,9011
Non-polymers6515
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Gibberellin receptor GID1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6467
Polymers40,9011
Non-polymers7466
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Gibberellin receptor GID1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4895
Polymers40,9011
Non-polymers5894
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Gibberellin receptor GID1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4895
Polymers40,9011
Non-polymers5894
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Gibberellin receptor GID1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4604
Polymers40,9011
Non-polymers5603
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Gibberellin receptor GID1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4895
Polymers40,9011
Non-polymers5894
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)82,9499
Polymers81,8012
Non-polymers1,1487
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-47 kcal/mol
Surface area22720 Å2
MethodPISA, PQS
8
A: Gibberellin receptor GID1
B: Gibberellin receptor GID1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,19713
Polymers81,8012
Non-polymers1,39611
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-41 kcal/mol
Surface area23730 Å2
MethodPISA, PQS
9
C: Gibberellin receptor GID1
D: Gibberellin receptor GID1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,97910
Polymers81,8012
Non-polymers1,1778
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-32 kcal/mol
Surface area23060 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)82.717, 134.142, 118.872
Angle α, β, γ (deg.)90.00, 105.20, 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, 1132 molecules

#2: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


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


Mass: 62.005 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: NO3
#4: Chemical
ChemComp-GA3 / GIBBERELLIN A3 / (1S,2S,4aR,4bR,7S,9aS,10S,10aR)-2,7-dihydroxy-1-methyl-8-methylidene-13-oxo-1,2,4b,5,6,7,8,9,10,10a-decahydro-4a,1-(epo xymethano)-7,9a-methanobenzo[a]azulene-10-carboxylic acid


Mass: 346.374 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C19H22O6
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


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


Mass: 18.015 Da / Num. of mol.: 1106 / 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: 0.224 °
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: RAYONIX MX225HE / Detector: CCD / Date: Jul 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: 192246 / % possible obs: 97.6 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.054 / Χ2: 1.244 / Net I/σ(I): 27.585
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.365 / Num. unique all: 17227 / Χ2: 1.139 / % possible all: 87.5

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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
REFMAC5.2.0019phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EBL

3ebl


Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.935 / WRfactor Rfree: 0.237 / WRfactor Rwork: 0.195 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.822 / SU B: 3.436 / SU ML: 0.101 / SU R Cruickshank DPI: 0.14 / SU Rfree: 0.137 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.14 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23946 9618 5 %RANDOM
Rwork0.19716 ---
obs0.19925 181950 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: 99.85 Å2 / Biso mean: 31.091 Å2 / Biso min: 12.77 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å2-2.51 Å2
2--0.06 Å20 Å2
3----1.54 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14510 0 256 1106 15872
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02115196
X-RAY DIFFRACTIONr_angle_refined_deg1.4881.95820724
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.97951853
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.58822.65717
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.702152239
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0915127
X-RAY DIFFRACTIONr_chiral_restr0.0930.22255
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211808
X-RAY DIFFRACTIONr_nbd_refined0.1990.27267
X-RAY DIFFRACTIONr_nbtor_refined0.3120.210318
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.21212
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0810.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1160.221
X-RAY DIFFRACTIONr_mcbond_it0.8911.59509
X-RAY DIFFRACTIONr_mcangle_it1.496214866
X-RAY DIFFRACTIONr_scbond_it2.10236456
X-RAY DIFFRACTIONr_scangle_it3.0494.55858
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 638 -
Rwork0.263 11850 -
all-12488 -
obs--100 %

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