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- PDB-7wun: Crystal structure of UBR bof from PRT6 (RSG) -

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Basic information

Entry
Database: PDB / ID: 7wun
TitleCrystal structure of UBR bof from PRT6 (RSG)
Components
  • 3-mer peptide
  • E3 ubiquitin-protein ligase
KeywordsLIGASE / E3 ligase UBR Box PRT6
Function / homology
Function and homology information


ubiquitin-dependent protein catabolic process via the N-end rule pathway / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity / protein ubiquitination / zinc ion binding
Similarity search - Function
E3 ubiquitin-protein ligase UBR1-like / Putative zinc finger in N-recognin (UBR box) / Zinc finger, UBR-type / Zinc finger UBR-type profile. / Putative zinc finger in N-recognin, a recognition component of the N-end rule pathway
Similarity search - Domain/homology
E3 ubiquitin-protein ligase
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
Oryza sativa (Asian cultivated rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsHo, M.C. / Cao, C.C.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Academia Sinica (Taiwan) Taiwan
CitationJournal: To Be Published
Title: Crystal structure of UBR box from PRT6
Authors: Ho, M.C. / Cao, J.J.
History
DepositionFeb 8, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 8, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: 3-mer peptide
A: E3 ubiquitin-protein ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,4355
Polymers8,2392
Non-polymers1963
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area530 Å2
ΔGint1 kcal/mol
Surface area4240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.803, 29.803, 114.755
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein/peptide 3-mer peptide


Mass: 319.339 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Oryza sativa (Asian cultivated rice)
#2: Protein E3 ubiquitin-protein ligase / PRT6


Mass: 7919.854 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice)
Gene: Os01g0148000, OSNPB_010148000 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0P0UY23, RING-type E3 ubiquitin transferase
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 1.79 Å3/Da / Density % sol: 31.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1M sodium citrate, 200mM NaCl, 0.1M Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.53→50 Å / Num. obs: 9542 / % possible obs: 99.2 % / Redundancy: 8.6 % / Biso Wilson estimate: 12.18 Å2 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.041 / Rrim(I) all: 0.123 / Χ2: 1.247 / Net I/σ(I): 7.4 / Num. measured all: 82066
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.53-1.564.10.5194180.8340.240.5780.45888.4
1.56-1.584.60.5634440.8370.2560.6240.596.9
1.58-1.625.40.54670.9390.2180.5490.55399.8
1.62-1.656.80.5534710.910.2220.5980.563100
1.65-1.687.60.4114520.9780.1570.440.602100
1.68-1.728.70.4294760.9580.1520.4560.635100
1.72-1.779.90.4054710.970.1360.4280.623100
1.77-1.81100.3744500.970.1250.3950.638100
1.81-1.8710.20.2934990.9810.0960.3090.75599.8
1.87-1.9310.30.2764460.9760.090.290.807100
1.93-210.10.2224980.9880.0730.2340.946100
2-2.0810.20.184600.9890.0590.191.021100
2.08-2.179.80.1524810.990.0510.1611.091100
2.17-2.299.90.1284800.9950.0430.1351.299100
2.29-2.439.60.1194760.9950.0410.1261.42599.8
2.43-2.629.40.1064880.9970.0370.1121.622100
2.62-2.889.10.0974900.9960.0350.1032.04100
2.88-3.38.80.0755060.9980.0270.082.461100
3.3-4.158.50.0535000.9980.0190.0562.614100
4.15-5080.0525690.9990.020.0562.82198.8

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: D_1300027541

Resolution: 1.53→23.54 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 18.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1861 951 10.03 %
Rwork0.1673 8531 -
obs0.1692 9482 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 52.89 Å2 / Biso mean: 17.8143 Å2 / Biso min: 8.9 Å2
Refinement stepCycle: final / Resolution: 1.53→23.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms558 0 3 85 646
Biso mean--12.97 27.15 -
Num. residues----73
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.53-1.610.23641250.22461122124794
1.61-1.710.21541280.17111199132799
1.71-1.840.17881340.160712091343100
1.84-2.030.19131340.145412011335100
2.03-2.320.1671380.149712281366100
2.32-2.920.19551410.178612411382100
2.93-23.540.17551510.167813311482100

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