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- PDB-3vxk: Crystal structure of OsD14 -

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Basic information

Entry
Database: PDB / ID: 3vxk
TitleCrystal structure of OsD14
ComponentsDwarf 88 esterase
KeywordsHYDROLASE / alpha/beta-hydrolase fold
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: 1.75 Å
AuthorsXue, Y.-L. / Miyakawa, T. / Hou, F. / Qin, H.-M. / Tanokura, M.
CitationJournal: Nat Commun / Year: 2013
Title: Molecular mechanism of strigolactone perception by DWARF14
Authors: Nakamura, H. / Xue, Y.-L. / Miyakawa, T. / Hou, F. / Qin, H.-M. / Fukui, K. / Shi, X. / Ito, E. / Ito, S. / Park, S.-H. / Miyauchi, Y. / Asano, A. / Totsuka, N. / Ueda, T. / Tanokura, M. / Asami, T.
History
DepositionSep 18, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2013Group: Database references
Revision 1.2Apr 30, 2014Group: Database references
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Nov 8, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)60,0492
Polymers60,0492
Non-polymers00
Water6,125340
1
A: Dwarf 88 esterase


Theoretical massNumber of molelcules
Total (without water)30,0241
Polymers30,0241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dwarf 88 esterase


Theoretical massNumber of molelcules
Total (without water)30,0241
Polymers30,0241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.14, 88.72, 118.61
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Dwarf 88 esterase / ALPHA/BETA HYDROLASE / alpha/beta fold family protein / expressed / Os03g0203200 protein / cDNA ...ALPHA/BETA HYDROLASE / alpha/beta fold family protein / expressed / Os03g0203200 protein / cDNA clone J023064N24 / full insert sequence


Mass: 30024.361 Da / Num. of mol.: 2 / Fragment: UNP residues 54-318
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice)
Gene: D88, Os03g0203200, LOC_Os03g10620 / Production host: Escherichia coli (E. coli) / References: UniProt: Q10QA5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / 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: 2.11 Å3/Da / Density % sol: 41.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 8% PEG 20000, 2% 1,4-dioxane, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 26, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→20 Å / Num. obs: 51922 / Redundancy: 7.1 % / Rsym value: 0.076 / Net I/σ(I): 22
Reflection shellResolution: 1.75→1.8 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 6.5 / Rsym value: 0.337

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Processing

Software
NameVersionClassification
SERGUIdata collection
MOLREPphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WOM

1wom


Resolution: 1.75→20 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.916 / SU B: 2.172 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22261 2643 5.1 %RANDOM
Rwork0.1807 ---
obs0.18283 49279 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.061 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20 Å20 Å2
2---0.52 Å20 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4074 0 0 340 4414
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0224164
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9331.9585674
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1795524
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.18122.043186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.57315644
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5031542
X-RAY DIFFRACTIONr_chiral_restr0.1530.2658
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213190
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2981.52618
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.16524216
X-RAY DIFFRACTIONr_scbond_it3.5431546
X-RAY DIFFRACTIONr_scangle_it5.4854.51458
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.751→1.796 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 195 -
Rwork0.202 3559 -
obs--99.08 %

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