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- PDB-8hmg: The open state of RGLG2-VWA -

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Open data


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Basic information

Entry
Database: PDB / ID: 8hmg
TitleThe open state of RGLG2-VWA
ComponentsE3 ubiquitin-protein ligase RGLG2
KeywordsPLANT PROTEIN / E3 ubiquitin ligase / Allosteric regulation / Calcium ions binding
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 / zinc ion binding / nucleus / 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: 2.81 Å
AuthorsWang, Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Ca2+-based Allosteric Switches and Shape Shifting in RGLG1 VWA domain
Authors: Wang, Q.
History
DepositionDec 3, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 6, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase RGLG2
B: E3 ubiquitin-protein ligase RGLG2
C: E3 ubiquitin-protein ligase RGLG2
D: E3 ubiquitin-protein ligase RGLG2
E: E3 ubiquitin-protein ligase RGLG2
F: E3 ubiquitin-protein ligase RGLG2
G: E3 ubiquitin-protein ligase RGLG2
H: E3 ubiquitin-protein ligase RGLG2
I: E3 ubiquitin-protein ligase RGLG2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)309,67365
Polymers306,4519
Non-polymers3,22256
Water8,593477
1
A: E3 ubiquitin-protein ligase RGLG2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3877
Polymers34,0501
Non-polymers3376
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: E3 ubiquitin-protein ligase RGLG2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3877
Polymers34,0501
Non-polymers3376
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: E3 ubiquitin-protein ligase RGLG2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5799
Polymers34,0501
Non-polymers5298
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: E3 ubiquitin-protein ligase RGLG2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4838
Polymers34,0501
Non-polymers4337
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: E3 ubiquitin-protein ligase RGLG2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3877
Polymers34,0501
Non-polymers3376
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: E3 ubiquitin-protein ligase RGLG2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2916
Polymers34,0501
Non-polymers2415
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: E3 ubiquitin-protein ligase RGLG2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2916
Polymers34,0501
Non-polymers2415
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: E3 ubiquitin-protein ligase RGLG2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3877
Polymers34,0501
Non-polymers3376
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: E3 ubiquitin-protein ligase RGLG2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4838
Polymers34,0501
Non-polymers4337
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)244.410, 244.410, 63.650
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
55
66
77
88
99
1010
1111
1212
1313
1414
1515
1616
1717
1818
1919
2020
2121
2222
2323
2424
2525
2626
2727
2828
2929
3030
3131
3232
3333
3434
3535
3636

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36

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Components

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


Mass: 34050.121 Da / Num. of mol.: 9 / 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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 477 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.58 Å3/Da / Density % sol: 65.66 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 100 mM Tris-HCl, pH 7.5, 200 mM ammonium sulfate, 20% polyethylene glycol 4000

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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 315 / Detector: CCD / Date: May 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.81→49.81 Å / Num. obs: 103535 / % possible obs: 99.91 % / Redundancy: 10.43 % / CC1/2: 0.996 / Net I/σ(I): 11
Reflection shellResolution: 2.81→2.86 Å / Num. unique obs: 5094 / CC1/2: 0.734

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PHENIXmodel building
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.81→49.81 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / SU B: 13.232 / SU ML: 0.233 / Cross valid method: THROUGHOUT / ESU R: 0.638 / ESU R Free: 0.275 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20816 5115 4.9 %RANDOM
Rwork0.18343 ---
obs0.18468 98418 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 66.6 Å2
Baniso -1Baniso -2Baniso -3
1--2.54 Å2-1.27 Å20 Å2
2---2.54 Å20 Å2
3---8.24 Å2
Refinement stepCycle: 1 / Resolution: 2.81→49.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20433 0 136 477 21046
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01321151
X-RAY DIFFRACTIONr_bond_other_d0.0010.01519611
X-RAY DIFFRACTIONr_angle_refined_deg1.4791.64328360
X-RAY DIFFRACTIONr_angle_other_deg1.2761.57945220
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.47652588
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.54723.2461146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.211153575
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.74415126
X-RAY DIFFRACTIONr_chiral_restr0.0660.22752
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0223909
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024823
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.0216.74210463
X-RAY DIFFRACTIONr_mcbond_other5.9996.74810408
X-RAY DIFFRACTIONr_mcangle_it8.96410.12612960
X-RAY DIFFRACTIONr_mcangle_other8.96410.12712961
X-RAY DIFFRACTIONr_scbond_it6.4167.32610688
X-RAY DIFFRACTIONr_scbond_other6.3237.30210592
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.72710.7115281
X-RAY DIFFRACTIONr_long_range_B_refined14.23378.90122900
X-RAY DIFFRACTIONr_long_range_B_other14.21778.90122852
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A95070.05
12B95070.05
21A94560.05
22C94560.05
31A94770.05
32D94770.05
41A93910.05
42E93910.05
51A94490.05
52F94490.05
61A94920.05
62G94920.05
71A95250.04
72H95250.04
81A95030.05
82I95030.05
91B95020.05
92C95020.05
101B95580.05
102D95580.05
111B95210.05
112E95210.05
121B95170.05
122F95170.05
131B94730.05
132G94730.05
141B95600.04
142H95600.04
151B96240.05
152I96240.05
161C94460.06
162D94460.06
171C94880.05
172E94880.05
181C94720.05
182F94720.05
191C94010.06
192G94010.06
201C95490.05
202H95490.05
211C94950.05
212I94950.05
221D94410.05
222E94410.05
231D94450.05
232F94450.05
241D94260.05
242G94260.05
251D95120.05
252H95120.05
261D95380.05
262I95380.05
271E94640.05
272F94640.05
281E94360.04
282G94360.04
291E94660.05
292H94660.05
301E95280.05
302I95280.05
311F93710.06
312G93710.06
321F94280.06
322H94280.06
331F95140.05
332I95140.05
341G94630.04
342H94630.04
351G95040.05
352I95040.05
361H95440.05
362I95440.05
LS refinement shellResolution: 2.81→2.883 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 380 -
Rwork0.367 7334 -
obs--99.96 %

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