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- PDB-4ih9: Crystal structure of rice DWARF14 (D14) -

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Basic information

Entry
Database: PDB / ID: 4ih9
TitleCrystal structure of rice DWARF14 (D14)
ComponentsDwarf 88 esterase
KeywordsHYDROLASE / strigolactone receptor / alpha/beta hydrolase
Function / homology
Function and homology information


strigolactone biosynthetic process / secondary shoot formation / Hydrolases; Acting on ester bonds / hydrolase activity / nucleus / cytoplasm
Similarity search - Function
Alpha/beta hydrolase family / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Strigolactone esterase D14
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsZhou, X.E. / Zhao, L.-H. / Wu, Z.-S. / Yi, W. / Li, S. / Li, Y. / Xu, Y. / Xu, T.-H. / Liu, Y. / Chen, R.-Z. ...Zhou, X.E. / Zhao, L.-H. / Wu, Z.-S. / Yi, W. / Li, S. / Li, Y. / Xu, Y. / Xu, T.-H. / Liu, Y. / Chen, R.-Z. / Kovach, A. / Kang, Y. / Hou, L. / He, Y. / Zhang, C. / Melcher, K. / Xu, H.E.
CitationJournal: Cell Res. / Year: 2013
Title: Crystal structures of two phytohormone signal-transducing alpha / beta hydrolases: karrikin-signaling KAI2 and strigolactone-signaling DWARF14.
Authors: Zhao, L.H. / Zhou, X.E. / Wu, Z.S. / Yi, W. / Xu, Y. / Li, S. / Xu, T.H. / Liu, Y. / Chen, R.Z. / Kovach, A. / Kang, Y. / Hou, L. / He, Y. / Xie, C. / Song, W. / Zhong, D. / Xu, Y. / Wang, Y. ...Authors: Zhao, L.H. / Zhou, X.E. / Wu, Z.S. / Yi, W. / Xu, Y. / Li, S. / Xu, T.H. / Liu, Y. / Chen, R.Z. / Kovach, A. / Kang, Y. / Hou, L. / He, Y. / Xie, C. / Song, W. / Zhong, D. / Xu, Y. / Wang, Y. / Li, J. / Zhang, C. / Melcher, K. / Xu, H.E.
History
DepositionDec 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2013Group: Database references
Revision 1.2Sep 20, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dwarf 88 esterase
B: Dwarf 88 esterase


Theoretical massNumber of molelcules
Total (without water)58,6992
Polymers58,6992
Non-polymers00
Water6,702372
1
A: Dwarf 88 esterase


Theoretical massNumber of molelcules
Total (without water)29,3501
Polymers29,3501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dwarf 88 esterase


Theoretical massNumber of molelcules
Total (without water)29,3501
Polymers29,3501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.196, 88.460, 121.228
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 Dwarf 88 esterase / Hydrolase / alpha/beta fold family protein / expressed / Os03g0203200 protein / cDNA clone ...Hydrolase / alpha/beta fold family protein / expressed / Os03g0203200 protein / cDNA clone J023064N24 / full insert sequence


Mass: 29349.707 Da / Num. of mol.: 2 / Fragment: UNP residues 51-318
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice)
Gene: D14, D88, LOC_Os03g10620, Os03g0203200 / Plasmid: pETDuet1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q10QA5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 372 / 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: 2.2 Å3/Da / Density % sol: 44.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: PEG6000, MPD, pH 7.5, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 9, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→40 Å / Num. all: 76211 / Num. obs: 76002 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0072refinement
PDB_EXTRACT3.11data extraction
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IH1

4ih1


Resolution: 1.55→40 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.952 / Occupancy max: 1 / Occupancy min: 1 / SU B: 1.338 / SU ML: 0.049 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.083 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.197 5487 7.2 %RANDOM
Rwork0.1789 ---
obs0.1802 75984 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 53.15 Å2 / Biso mean: 15.7356 Å2 / Biso min: 5.79 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0.06 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.55→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4100 0 0 372 4472
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224200
X-RAY DIFFRACTIONr_bond_other_d0.0010.022803
X-RAY DIFFRACTIONr_angle_refined_deg1.2351.9575719
X-RAY DIFFRACTIONr_angle_other_deg0.84736771
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8295530
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.64522.043186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.00915653
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.361542
X-RAY DIFFRACTIONr_chiral_restr0.0770.2663
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214724
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02922
X-RAY DIFFRACTIONr_mcbond_it0.8531.52645
X-RAY DIFFRACTIONr_mcbond_other0.211.51075
X-RAY DIFFRACTIONr_mcangle_it1.64724255
X-RAY DIFFRACTIONr_scbond_it2.49831555
X-RAY DIFFRACTIONr_scangle_it4.0414.51464
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 412 -
Rwork0.265 5092 -
all-5504 -
obs--99.98 %

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