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- PDB-8hmh: The closed state of RGLG2-VWA -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8hmh
TitleThe closed state of RGLG2-VWA
ComponentsE3 ubiquitin-protein ligase RGLG2
KeywordsSTRUCTURAL PROTEIN / closed state / calcium ions / PLANT PROTEIN / TRANSFERASE
Function / homology
Function and homology information


auxin metabolic process / negative regulation of response to water deprivation / cytokinin metabolic process / abscisic acid-activated signaling pathway / protein K63-linked ubiquitination / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / nucleus / metal ion binding / plasma membrane
Similarity search - Function
E3 ubiquitin-protein ligase RGLG, RING finger, plant / : / 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 RGLG2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 Å
AuthorsWang, Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Biochim Biophys Acta Proteins Proteom / Year: 2024
Title: The regulation of RGLG2-VWA by Ca 2+ ions.
Authors: Zhang, M. / Zhang, J. / Liang, Y. / Tian, S. / Xie, S. / Zhou, T. / Wang, Q.
History
DepositionDec 3, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 3, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 13, 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

Downloads & links

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Assembly

Deposited unit
B: E3 ubiquitin-protein ligase RGLG2
A: E3 ubiquitin-protein ligase RGLG2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9486
Polymers68,8512
Non-polymers974
Water61334
1
B: E3 ubiquitin-protein ligase RGLG2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4743
Polymers34,4251
Non-polymers492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-8 kcal/mol
Surface area12330 Å2
MethodPISA
2
A: E3 ubiquitin-protein ligase RGLG2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4743
Polymers34,4251
Non-polymers492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-8 kcal/mol
Surface area11820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.960, 62.960, 155.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein E3 ubiquitin-protein ligase RGLG2 / RING domain ligase 2


Mass: 34425.277 Da / Num. of mol.: 2 / Fragment: VWA domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: RGLG2, At5g14420, F18O22.210 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9LY87, RING-type E3 ubiquitin transferase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O
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: 2.26 Å3/Da / Density % sol: 44.88 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 200 mM magnesium chloride, 30% PEG 4000, 100 mM Tris-HCl, PH8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: AichiSR / Beamline: BL2S1 / Wavelength: 0.979183 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 2.56→48.873 Å / Num. obs: 19226 / % possible obs: 99 % / Redundancy: 13.9 % / CC1/2: 0.994 / Net I/σ(I): 11.3
Reflection shellResolution: 2.56→2.63 Å / Mean I/σ(I) obs: 2.1 / Num. unique obs: 962 / CC1/2: 0.722

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PHENIXmodel building
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.56→48.873 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 30.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2459 947 4.94 %
Rwork0.1866 --
obs0.1896 19189 98.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.56→48.873 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4202 0 4 34 4240
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0274295
X-RAY DIFFRACTIONf_angle_d1.4625824
X-RAY DIFFRACTIONf_dihedral_angle_d15.2491588
X-RAY DIFFRACTIONf_chiral_restr0.051644
X-RAY DIFFRACTIONf_plane_restr0.011774
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5601-2.69510.3261240.28262607X-RAY DIFFRACTION99
2.6951-2.8640.30741410.25522580X-RAY DIFFRACTION98
2.864-3.0850.34751110.24412594X-RAY DIFFRACTION98
3.085-3.39540.26151380.2042597X-RAY DIFFRACTION99
3.3954-3.88660.24121320.18522653X-RAY DIFFRACTION100
3.8866-4.8960.23831310.14792598X-RAY DIFFRACTION99
4.896-48.870.20751700.16682613X-RAY DIFFRACTION99

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