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- PDB-4ih4: Crystal structure of Arabidopsis DWARF14 orthologue, AtD14 -

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Basic information

Entry
Database: PDB / ID: 4ih4
TitleCrystal structure of Arabidopsis DWARF14 orthologue, AtD14
ComponentsAT3g03990/T11I18_10
KeywordsHYDROLASE / strigolactone receptor / alpha/beta hydrolase
Function / homology
Function and homology information


cellular response to strigolactone / 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 speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 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: AT3g03990/T11I18_10
B: AT3g03990/T11I18_10
C: AT3g03990/T11I18_10
D: AT3g03990/T11I18_10


Theoretical massNumber of molelcules
Total (without water)118,6154
Polymers118,6154
Non-polymers00
Water00
1
A: AT3g03990/T11I18_10


Theoretical massNumber of molelcules
Total (without water)29,6541
Polymers29,6541
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: AT3g03990/T11I18_10


Theoretical massNumber of molelcules
Total (without water)29,6541
Polymers29,6541
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: AT3g03990/T11I18_10


Theoretical massNumber of molelcules
Total (without water)29,6541
Polymers29,6541
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: AT3g03990/T11I18_10


Theoretical massNumber of molelcules
Total (without water)29,6541
Polymers29,6541
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)184.856, 44.629, 160.967
Angle α, β, γ (deg.)90.000, 121.070, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
AT3g03990/T11I18_10 / Alpha/beta-hydrolase domain-containing protein / T11I18.10 protein


Mass: 29653.727 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At3g03990, AtD14, T11I18.10 / Plasmid: pETDuet1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q9SQR3

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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: 2.4 Å3/Da / Density % sol: 48.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.5
Details: PEG4000, MgCl2, pH 8.5, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 21, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→30 Å / Num. obs: 12471 / % possible obs: 83.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Rmerge(I) obs: 0.204 / Χ2: 1.042 / Net I/σ(I): 4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.5-3.6240.55712351.082185.6
3.62-3.774.10.49412640.897185.2
3.77-3.9440.38112490.985185.2
3.94-4.154.10.26912600.986185.5
4.15-4.414.10.20712571.11185.3
4.41-4.754.10.18212211.07183.9
4.75-5.224.20.17612721.061184.5
5.22-5.974.20.17212341.004182.5
5.97-7.54.30.14512501.046182.3
7.5-304.10.06512291.181178.6

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Processing

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

4ih1


Resolution: 3.5→30 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 1984
RfactorNum. reflection% reflection
Rfree0.3363 686 4.7 %
Rwork0.2785 --
all-14681 -
obs-9439 64.3 %
Solvent computationBsol: -7.122 Å2
Displacement parametersBiso max: 84.56 Å2 / Biso mean: 37.0413 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-7.644 Å20 Å214.486 Å2
2---1.045 Å20 Å2
3----6.599 Å2
Refinement stepCycle: LAST / Resolution: 3.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8160 0 0 0 8160
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it0.9521.5
X-RAY DIFFRACTIONc_scbond_it0.9262
X-RAY DIFFRACTIONc_mcangle_it1.7161.5
X-RAY DIFFRACTIONc_scangle_it1.5332
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2dna-rna_rep.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4ion.param
X-RAY DIFFRACTION5carbohydrate.param

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