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- PDB-3w06: Crystal structure of Arabidopsis thaliana DWARF14 Like (AtD14L) -

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Basic information

Entry
Database: PDB / ID: 3w06
TitleCrystal structure of Arabidopsis thaliana DWARF14 Like (AtD14L)
ComponentsHydrolase, alpha/beta fold family protein
KeywordsHYDROLASE / KARRIKIN SIGNALING / ALPHA/BETA HYDROLASE / KARRIKIN BINDING
Function / homology
Function and homology information


de-etiolation / response to karrikin / photomorphogenesis / hydrolase activity / nucleus / cytosol
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
Probable esterase KAI2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 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: Hydrolase, alpha/beta fold family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3427
Polymers29,9701
Non-polymers3726
Water5,477304
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.953, 55.603, 53.128
Angle α, β, γ (deg.)90.00, 115.81, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Hydrolase, alpha/beta fold family protein / Putative uncharacterized protein AT4g37470 / Putative uncharacterized protein At4g37470 / Putative ...Putative uncharacterized protein AT4g37470 / Putative uncharacterized protein At4g37470 / Putative uncharacterized protein F6G17.120


Mass: 29970.076 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AT4g37470, F6G17.120 / Plasmid: PET49B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 STAR (DE3) / References: UniProt: Q9SZU7
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / 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: 2.26 Å3/Da / Density % sol: 45.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.0M AMMONIUM SULFATE, 0.2M BICINE, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: May 18, 2011 / Details: mirrors
RadiationMonochromator: Rotated-inclined double-crystal monochromator , Si (111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.15→50 Å / Num. all: 94807 / Num. obs: 90920 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rsym value: 0.069
Reflection shellResolution: 1.15→1.19 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 8782 / Rsym value: 0.535 / % possible all: 93.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3W04

3w04


Resolution: 1.15→47.83 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.968 / SU B: 0.942 / SU ML: 0.02 / Cross valid method: THROUGHOUT / ESU R: 0.032 / ESU R Free: 0.034 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1621 4538 5 %RANDOM
Rwork0.13159 ---
obs0.13313 86188 95.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.826 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å2-0.01 Å2
2--0.1 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.15→47.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2070 0 24 304 2398
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222401
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6391.963297
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9955324
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.37624.464112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.4315394
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4741514
X-RAY DIFFRACTIONr_chiral_restr0.0890.2373
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211890
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_it2.8511.51486
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.02322452
X-RAY DIFFRACTIONr_scbond_it6.3043915
X-RAY DIFFRACTIONr_scangle_it8.6144.5834
X-RAY DIFFRACTIONr_rigid_bond_restr3.39332401
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.15→1.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 312 -
Rwork0.195 6117 -
obs-6117 91.82 %

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