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- PDB-7tvw: Crystal structure of Arabidopsis thaliana DLK2 -

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Basic information

Entry
Database: PDB / ID: 7tvw
TitleCrystal structure of Arabidopsis thaliana DLK2
ComponentsAlpha/beta-Hydrolases superfamily protein
KeywordsHYDROLASE / Sesquiterpene lactone perception
Function / homologyalpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / hydrolase activity / nucleus / cytoplasm / Alpha/beta-Hydrolases superfamily protein
Function and homology information
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.48 Å
AuthorsBurger, M. / Chory, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Plant Direct / Year: 2022
Title: Crystal structure of Arabidopsis DWARF14-LIKE2 (DLK2) reveals a distinct substrate binding pocket architecture.
Authors: Burger, M. / Honda, K. / Kondoh, Y. / Hong, S. / Watanabe, N. / Osada, H. / Chory, J.
History
DepositionFeb 6, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha/beta-Hydrolases superfamily protein


Theoretical massNumber of molelcules
Total (without water)30,2081
Polymers30,2081
Non-polymers00
Water5,783321
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.560, 84.590, 76.880
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Alpha/beta-Hydrolases superfamily protein / At3g24420 / Hydrolase-like protein / Uncharacterized protein At3g24420 / D14-LIKE2


Mass: 30207.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At3g24420 / Plasmid: pGEX4T3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9LK01
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 321 / 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: 2.14 Å3/Da / Density % sol: 42.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tris, 1.9 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 13, 2017 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.48→42.295 Å / Num. obs: 43371 / % possible obs: 99.7 % / Redundancy: 7.5 % / Biso Wilson estimate: 14.65 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.07077 / Net I/σ(I): 17.42
Reflection shellResolution: 1.48→1.533 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.7296 / Num. unique obs: 4281 / CC1/2: 0.881 / CC star: 0.968 / % possible all: 99.35

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IH1

4ih1


Resolution: 1.48→42.295 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1884 2180 5.03 %
Rwork0.1637 41188 -
obs0.165 43368 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 103.46 Å2 / Biso mean: 20.8821 Å2 / Biso min: 6.43 Å2
Refinement stepCycle: final / Resolution: 1.48→42.295 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 0 321 2370
Biso mean---33.05 -
Num. residues----265
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072141
X-RAY DIFFRACTIONf_angle_d1.1042907
X-RAY DIFFRACTIONf_chiral_restr0.045332
X-RAY DIFFRACTIONf_plane_restr0.005371
X-RAY DIFFRACTIONf_dihedral_angle_d13.232797
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.48-1.51220.2871130.2801253899
1.5122-1.54740.27371460.24362521100
1.5474-1.58610.26451310.22832562100
1.5861-1.6290.2431130.2062576100
1.629-1.67690.22741310.18682542100
1.6769-1.7310.23421320.17962589100
1.731-1.79290.2231470.17472515100
1.7929-1.86470.19941360.17762568100
1.8647-1.94960.20691370.17232557100
1.9496-2.05230.18561530.16312560100
2.0523-2.18090.18841280.16132582100
2.1809-2.34930.1821400.1564257699
2.3493-2.58570.16951420.1635256599
2.5857-2.95980.19851310.16942603100
2.9598-3.72860.20121520.1502259999
3.7286-42.2950.13661480.13212735100

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