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- PDB-7xwd: Apo-AtPRT6 UBR box -

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Basic information

Entry
Database: PDB / ID: 7xwd
TitleApo-AtPRT6 UBR box
ComponentsE3 ubiquitin-protein ligase PRT6
KeywordsLIGASE / PRT6 / UBR box / E3 ubiquitin ligase / Arabidopsis thaliana
Function / homology
Function and homology information


regulation of seed germination / ubiquitin-dependent protein catabolic process via the N-end rule pathway / regulation of lipid catabolic process / response to abscisic acid / defense response to fungus / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / ubiquitin-dependent protein catabolic process / protein ubiquitination ...regulation of seed germination / ubiquitin-dependent protein catabolic process via the N-end rule pathway / regulation of lipid catabolic process / response to abscisic acid / defense response to fungus / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / ubiquitin-dependent protein catabolic process / protein ubiquitination / defense response to bacterium / zinc ion binding
Similarity search - Function
E3 ubiquitin-protein ligase ELL-like / E3 ubiquitin-protein ligase UBR-like, C-terminal / Proteolysis_6 C-terminal / E3 ubiquitin-protein ligase UBR1-like, winged-helix domain / E3 ubiquitin-protein ligase UBR1-like / Putative zinc finger in N-recognin (UBR box) / Zinc finger, UBR-type / Zinc finger UBR-type profile. / Putative zinc finger in N-recognin, a recognition component of the N-end rule pathway / Zinc finger, RING/FYVE/PHD-type / Winged helix DNA-binding domain superfamily
Similarity search - Domain/homology
E3 ubiquitin-protein ligase PRT6
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.396 Å
AuthorsKim, L. / Song, H.K.
Funding support Korea, Republic Of, 3items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2020R1A2C3008285 Korea, Republic Of
National Research Foundation (NRF, Korea)2021M3A9I4030068 Korea, Republic Of
National Research Foundation (NRF, Korea)2021R1A6A1A10045235 Korea, Republic Of
CitationJournal: To Be Published
Title: Structural analyses of plant PRT6-UBR box for Cys-Arg/N-degron pathway and insights into the plant submergence resistance
Authors: Kim, L. / Lin, C.C. / Lin, T.J. / Cao, Y.C. / Chen, M.C. / Chou, M.Y. / Lin, W.H. / Kim, M. / Wu, J.L. / Shih, M.C. / Song, H.K. / Ho, M.C.
History
DepositionMay 26, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase PRT6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8014
Polymers7,6041
Non-polymers1963
Water00
1
A: E3 ubiquitin-protein ligase PRT6
hetero molecules

A: E3 ubiquitin-protein ligase PRT6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6018
Polymers15,2092
Non-polymers3926
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x+1/2,y,-z+3/41
Buried area1170 Å2
ΔGint-10 kcal/mol
Surface area6800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.165, 87.165, 74.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein E3 ubiquitin-protein ligase PRT6 / Protein GREENING AFTER EXTENDED DARKNESS 1 / Protein PROTEOLYSIS 6 / RING-type E3 ubiquitin transferase PRT6


Mass: 7604.326 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress)
Gene: PRT6, CER3, GED1, At5g02310/At5g02300, T1E22.70/T1E22.60
Production host: Escherichia coli (E. coli)
References: UniProt: F4KCC2, RING-type E3 ubiquitin transferase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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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: 4.68 Å3/Da / Density % sol: 73.7 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.6M ammonium sulfate, 0.1 M sodium HEPES pH 7.5, 0.1 M NaCl

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Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.396→43.583 Å / Num. obs: 5882 / % possible obs: 99.88 % / Redundancy: 2 % / CC1/2: 0.997 / Net I/σ(I): 14.06
Reflection shellResolution: 2.396→2.482 Å / Num. unique obs: 573 / CC1/2: 0.815

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LHN

6lhn


Resolution: 2.396→43.583 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 29.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2685 589 10.02 %
Rwork0.2186 --
obs0.2236 5880 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.396→43.583 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms528 0 0 0 528
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011540
X-RAY DIFFRACTIONf_angle_d1.16734
X-RAY DIFFRACTIONf_dihedral_angle_d4.424308
X-RAY DIFFRACTIONf_chiral_restr0.05973
X-RAY DIFFRACTIONf_plane_restr0.008100
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3961-2.63720.27671420.27671275X-RAY DIFFRACTION100
2.6372-3.01880.29011450.27531308X-RAY DIFFRACTION100
3.0188-3.8030.27631460.22861316X-RAY DIFFRACTION100
3.803-43.5830.2581560.19351392X-RAY DIFFRACTION100

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