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- PDB-8xt5: The closed state of RGLG5-VWA -

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Basic information

Entry
Database: PDB / ID: 8xt5
TitleThe closed state of RGLG5-VWA
ComponentsE3 ubiquitin-protein ligase RGLG5
KeywordsPLANT PROTEIN / ligase / VWA domain
Function / homology
Function and homology information


positive regulation of abscisic acid-activated signaling pathway / abscisic acid-activated signaling pathway / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / protein ubiquitination / metal ion binding / nucleus / plasma membrane
Similarity search - Function
: / Copine, C-terminal / Copine / Zinc finger, C3HC4 type (RING finger) / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
E3 ubiquitin-protein ligase RGLG5
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.391 Å
AuthorsWang, Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structure of the E3 ubiquitin ligase RGLG5 VWA domain
Authors: Wang, Q.
History
DepositionJan 10, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase RGLG5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0693
Polymers31,9981
Non-polymers712
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area300 Å2
ΔGint-20 kcal/mol
Surface area12190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.998, 66.945, 84.884
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 E3 ubiquitin-protein ligase RGLG5 / RING domain ligase 5


Mass: 31997.697 Da / Num. of mol.: 1 / Fragment: VWA domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: RGLG5, At1g67800 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8LB88, RING-type E3 ubiquitin transferase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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 Å3/Da / Density % sol: 38.43 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 30% polyethylene glycol 8K, 0.5 M KCl, 0.1 M MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: AichiSR / Beamline: BL2S1 / Wavelength: 0.9789 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.39→26.857 Å / Num. obs: 51982 / % possible obs: 99.56 % / Redundancy: 12.5 % / Rrim(I) all: 0.065 / Net I/σ(I): 1.36
Reflection shellResolution: 1.39→1.42 Å / Num. unique obs: 3108 / CC1/2: 0.593

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Processing

SoftwareName: PHENIX / Version: 1.9_1692 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.391→26.857 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 16.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1839 2000 3.85 %
Rwork0.1554 --
obs0.1565 51982 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.391→26.857 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2109 0 2 229 2340
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122157
X-RAY DIFFRACTIONf_angle_d1.3692936
X-RAY DIFFRACTIONf_dihedral_angle_d13.159787
X-RAY DIFFRACTIONf_chiral_restr0.054327
X-RAY DIFFRACTIONf_plane_restr0.01392
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3911-1.42590.34661350.29243352X-RAY DIFFRACTION95
1.4259-1.46440.26891420.22423543X-RAY DIFFRACTION100
1.4644-1.50750.22741410.17163520X-RAY DIFFRACTION100
1.5075-1.55620.19171420.14623555X-RAY DIFFRACTION100
1.5562-1.61180.17451410.13393532X-RAY DIFFRACTION100
1.6118-1.67630.16271420.13093559X-RAY DIFFRACTION100
1.6763-1.75260.18111420.13943554X-RAY DIFFRACTION100
1.7526-1.84490.19421420.13823550X-RAY DIFFRACTION100
1.8449-1.96050.18641440.13523585X-RAY DIFFRACTION100
1.9605-2.11180.18991420.1433562X-RAY DIFFRACTION100
2.1118-2.32420.14711440.1433589X-RAY DIFFRACTION100
2.3242-2.66030.21091450.15683640X-RAY DIFFRACTION100
2.6603-3.35070.17561460.16633652X-RAY DIFFRACTION100
3.3507-26.8570.17711520.15873789X-RAY DIFFRACTION99

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