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- PDB-3w04: Crystal structure of Oryza sativa DWARF14 (D14) -

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Basic information

Entry
Database: PDB / ID: 3w04
TitleCrystal structure of Oryza sativa DWARF14 (D14)
ComponentsDwarf 88 esterase
KeywordsHYDROLASE / STRIGOLACTONE SIGNALING / ALPHA/BETA HYDROLASE / STRIGOLACTONE Hydrolysis
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: 1.45 Å
AuthorsKagiyama, M. / Hirano, Y. / Mori, T. / Kim, S.Y. / Kyozuka, J. / Seto, Y. / Yamaguchi, S. / Hakoshima, T.
CitationJournal: Genes Cells / Year: 2013
Title: Structures of D14 and D14L in the strigolactone and karrikin signaling pathways
Authors: Kagiyama, M. / Hirano, Y. / Mori, T. / Kim, S.Y. / Kyozuka, J. / Seto, Y. / Yamaguchi, S. / Hakoshima, T.
History
DepositionOct 19, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2013Group: 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: Dwarf 88 esterase
B: Dwarf 88 esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,29212
Polymers58,3832
Non-polymers90910
Water8,143452
1
A: Dwarf 88 esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4965
Polymers29,1921
Non-polymers3044
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dwarf 88 esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7967
Polymers29,1921
Non-polymers6056
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.988, 88.191, 121.231
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 / Hydrolase / alpha/beta fold family protein / expressed / Os03g0203200 protein


Mass: 29191.555 Da / Num. of mol.: 2 / Fragment: UNP residues 55-318
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice)
Gene: D88, LOC_Os03g10620, Os03g0203200 / Plasmid: PET47B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 STAR (DE3) / References: UniProt: Q10QA5
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 452 / 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: 44.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 8% PEG6000, 5% MPD, 0.1M Na-HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: May 23, 2010 / Details: mirros
RadiationMonochromator: Rotated-inclined double-crystal monochromator , Si (111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. all: 91864 / Num. obs: 91864 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Rsym value: 0.053
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 3.3 / Num. unique all: 9084 / Rsym value: 0.617 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WOM

1wom


Resolution: 1.45→25.62 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.006 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19378 4583 5 %RANDOM
Rwork0.16041 ---
obs0.16209 86870 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.313 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.45→25.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4073 0 59 452 4584
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0224362
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.541.9665956
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8065565
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.18622.135192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.2315680
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5931544
X-RAY DIFFRACTIONr_chiral_restr0.1760.2684
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0213340
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_it1.4661.52718
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.45524403
X-RAY DIFFRACTIONr_scbond_it3.52231644
X-RAY DIFFRACTIONr_scangle_it5.2644.51545
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.45→1.489 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 321 -
Rwork0.231 6305 -
obs--99.53 %

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