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- PDB-6k89: The closed state of RGLG1 VWA domain -

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Basic information

Entry
Database: PDB / ID: 6k89
TitleThe closed state of RGLG1 VWA domain
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: 1.689 Å
AuthorsWang, Q. / Wu, Y.
CitationJournal: To Be Published
Title: The closed state of RGLG1 VWA domain
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

Downloads & links

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Assembly

Deposited unit
B: E3 ubiquitin-protein ligase RGLG1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2123
Polymers33,1651
Non-polymers472
Water3,927218
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-12 kcal/mol
Surface area12380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.619, 72.935, 80.077
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: 33165.137 Da / Num. of mol.: 1
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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.06 Å3/Da / Density % sol: 40.43 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.1 M NaAc, 25%PEG4K, 8% isopropanol

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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: 1.7→50 Å / Num. obs: 30477 / % possible obs: 99.7 % / Redundancy: 12 % / Biso Wilson estimate: 24.8 Å2 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.042 / Rrim(I) all: 0.149 / Χ2: 0.456 / Net I/σ(I): 2.5 / Num. measured all: 367235
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.7-1.738.31.41214630.4760.5071.5040.3899.3
1.73-1.769.71.27815100.5830.4221.3470.38399.3
1.76-1.7910.31.21414840.6570.3891.2760.39499.5
1.79-1.8310.61.0215050.7820.3211.070.39699.5
1.83-1.8710.40.88914950.7790.2840.9350.39999.8
1.87-1.9110.90.72115020.8580.2250.7560.41499.5
1.91-1.9612.50.69414950.9190.2010.7230.42499.7
1.96-2.0212.80.58615160.9390.1680.610.42799.7
2.02-2.0713.10.54614930.9580.1550.5680.43799.7
2.07-2.1413.20.43515050.9680.1230.4520.43999.8
2.14-2.2213.20.35115270.9810.10.3650.43999.8
2.22-2.3113.10.30915130.9810.0880.3210.46399.9
2.31-2.4111.70.24715210.9820.0750.2590.45499.7
2.41-2.5413.50.22515220.9880.0630.2330.478100
2.54-2.713.70.18615300.9920.0520.1930.486100
2.7-2.9113.40.14315240.9950.040.1490.484100
2.91-3.213.10.11515600.9960.0330.1190.506100
3.2-3.6611.80.08515510.9960.0250.0880.52799.9
3.66-4.6113.40.07115790.9970.020.0730.564100
4.61-5011.90.06716820.9970.020.070.51799.8

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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: 1.689→40.038 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2307 1500 4.93 %
Rwork0.1878 28914 -
obs0.19 30414 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 67.39 Å2 / Biso mean: 29.1721 Å2 / Biso min: 14.62 Å2
Refinement stepCycle: final / Resolution: 1.689→40.038 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2208 0 2 218 2428
Biso mean--30.93 37.02 -
Num. residues----282
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062257
X-RAY DIFFRACTIONf_angle_d1.0363066
X-RAY DIFFRACTIONf_chiral_restr0.038341
X-RAY DIFFRACTIONf_plane_restr0.005407
X-RAY DIFFRACTIONf_dihedral_angle_d13.947839
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6888-1.74330.35111200.30432400252092
1.7433-1.80560.32231220.278925972719100
1.8056-1.87790.23751250.24992602272799
1.8779-1.96330.27541410.214126322773100
1.9633-2.06680.30391270.214726192746100
2.0668-2.19630.25531370.197226182755100
2.1963-2.36590.22381390.193826372776100
2.3659-2.60390.24761380.19126542792100
2.6039-2.98060.23511510.192426492800100
2.9806-3.75480.19851390.163926922831100
3.7548-40.04970.20511610.16428142975100

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