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- PDB-6k87: The closed state of RGLG1 VWA domain with MIDAS is occupied by water -

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Basic information

Entry
Database: PDB / ID: 6k87
TitleThe closed state of RGLG1 VWA domain with MIDAS is occupied by water
ComponentsE3 ubiquitin-protein ligase RGLG1
KeywordsTRANSFERASE / RGLG1 VWA closed
Function / homology
Function and homology information


negative regulation of response to water deprivation / positive regulation of abscisic acid-activated signaling pathway / 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 RGLG1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.502 Å
AuthorsWang, Q. / Wu, Y.
CitationJournal: To Be Published
Title: The closed state of RGLG1 VWA domain with MIDAS is occupied by water
Authors: Wang, Q. / Wu, Y.
History
DepositionJun 11, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: E3 ubiquitin-protein ligase RGLG1


Theoretical massNumber of molelcules
Total (without water)33,1071
Polymers33,1071
Non-polymers00
Water6,035335
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12800 Å2
Unit cell
Length a, b, c (Å)42.789, 73.690, 82.436
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein E3 ubiquitin-protein ligase RGLG1 / RING domain ligase 1


Mass: 33107.102 Da / Num. of mol.: 1 / Mutation: E378A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: RGLG1, At3g01650, F4P13.19 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9SS90, RING-type E3 ubiquitin transferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 335 / 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: 2.01 Å3/Da / Density % sol: 38.94 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 50 mM LiSO4, 50 mM NaSO4, 0.1 M Mes ph 6.5, 30%PEG8k

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: AichiSR / Beamline: BL2S1 / Wavelength: 0.978897 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978897 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 39569 / % possible obs: 93.6 % / Redundancy: 7.9 % / Biso Wilson estimate: 19.98 Å2 / Rmerge(I) obs: 0.189 / Rpim(I) all: 0.067 / Rrim(I) all: 0.201 / Χ2: 1.674 / Net I/σ(I): 3.5 / Num. measured all: 313357
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.5-1.536.20.94915040.2590.3711.0270.69672.9
1.53-1.556.50.87116010.5130.3290.9370.73577.6
1.55-1.586.40.84217260.5930.3210.9070.84982
1.58-1.627.50.79317610.60.280.8450.87185.7
1.62-1.657.80.73318700.7180.2560.7810.90689.4
1.65-1.698.10.71219440.7560.2480.7570.93292.3
1.69-1.738.10.65419520.7690.230.6960.97295.2
1.73-1.788.10.60620450.7590.2150.6461.08997.1
1.78-1.8380.56320700.810.2030.6011.13598.7
1.83-1.897.40.49120680.8360.1830.5271.29699.1
1.89-1.968.50.42220820.9010.1470.4491.47899.4
1.96-2.048.60.38720960.9040.1360.4121.60899.1
2.04-2.138.50.33720890.9330.1180.3591.72999.2
2.13-2.248.40.28820930.9490.1020.3072.02398.9
2.24-2.387.80.25320850.9580.0920.2712.09198.7
2.38-2.568.40.22820850.9710.080.2422.32698.9
2.56-2.828.70.20221240.9760.070.2152.51398.4
2.82-3.238.30.16920860.980.060.182.72397.7
3.23-4.077.90.13721110.9850.0490.1473.04796.8
4.07-508.10.1221770.9860.0430.1282.7294

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.502→37.978 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2289 1911 4.84 %
Rwork0.1927 37542 -
obs0.1943 39453 93.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 61.86 Å2 / Biso mean: 23.4102 Å2 / Biso min: 12.26 Å2
Refinement stepCycle: final / Resolution: 1.502→37.978 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2204 0 0 335 2539
Biso mean---31.09 -
Num. residues----282
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072253
X-RAY DIFFRACTIONf_angle_d1.0453061
X-RAY DIFFRACTIONf_chiral_restr0.038341
X-RAY DIFFRACTIONf_plane_restr0.006406
X-RAY DIFFRACTIONf_dihedral_angle_d13.685836
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5016-1.53920.34261060.29471854196066
1.5392-1.58080.29811340.27592269240381
1.5808-1.62730.28591370.25442425256286
1.6273-1.67990.28491400.23852560270091
1.6799-1.73990.30071420.24442704284695
1.7399-1.80960.28361180.22982806292498
1.8096-1.89190.28611520.22272826297899
1.8919-1.99170.2361390.19482849298899
1.9917-2.11640.19951270.19072867299499
2.1164-2.27980.19621410.18252847298899
2.2798-2.50920.23391380.19462878301699
2.5092-2.87220.22341550.19052836299198
2.8722-3.61820.20331350.18312882301798
3.6182-37.98990.21751470.16982939308695

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