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- PDB-3wio: Crystal structure of OSD14 in complex with hydroxy D-ring -

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Basic information

Entry
Database: PDB / ID: 3wio
TitleCrystal structure of OSD14 in complex with hydroxy D-ring
ComponentsProbable strigolactone esterase D14
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
(5R)-5-hydroxy-3-methylfuran-2(5H)-one / Strigolactone esterase D14
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 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 22, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 23, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2014Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / 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

Downloads & links

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Assembly

Deposited unit
A: Probable strigolactone esterase D14
B: Probable strigolactone esterase D14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1633
Polymers60,0492
Non-polymers1141
Water3,513195
1
A: Probable strigolactone esterase D14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1382
Polymers30,0241
Non-polymers1141
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Probable strigolactone esterase D14


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)48.380, 88.130, 119.020
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 Probable strigolactone esterase D14 / DWARF 88 ESTERASE / Protein DWARF-14 / Protein DWARF-88 / Protein HIGH-TILLERING DWARF 2


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: D14, D88, HTD2, LOC_Os03g10620, Os03g0203200 / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: Q10QA5, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-H3M / (5R)-5-hydroxy-3-methylfuran-2(5H)-one


Mass: 114.099 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 41.78 %
Crystal growTemperature: 277 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 277K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Mar 30, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 30394 / Redundancy: 7.1 % / Rsym value: 0.086 / Net I/σ(I): 20.4
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 7 % / Mean I/σ(I) obs: 5.2 / Rsym value: 0.43

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VXK

3vxk


Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.904 / SU B: 5.279 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.245 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1537 5.1 %RANDOM
Rwork0.188 ---
obs0.191 28858 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.01 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20 Å20 Å2
2---0.54 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4108 0 8 195 4311
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0224206
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8791.965729
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3075529
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.96322.043186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.73115653
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7511542
X-RAY DIFFRACTIONr_chiral_restr0.1280.2664
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213218
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_it1.051.52643
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.86524254
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.1331563
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.7644.51475
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 96 -
Rwork0.211 2047 -
obs--100 %

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