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- PDB-7wul: Crystal structure of UBR bof from PRT6 (RDG pH5.5) -

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Basic information

Entry
Database: PDB / ID: 7wul
TitleCrystal structure of UBR bof from PRT6 (RDG pH5.5)
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: 1.58 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)8,4635
Polymers8,2672
Non-polymers1963
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area560 Å2
ΔGint1 kcal/mol
Surface area4220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.802, 29.802, 114.856
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-346-

HOH

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Components

#1: Protein/peptide 3-mer peptide


Mass: 347.349 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.: 72 / 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: 1.78 Å3/Da / Density % sol: 30.94 %
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: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.58→30 Å / Num. obs: 8723 / % possible obs: 99.5 % / Redundancy: 7.6 % / Biso Wilson estimate: 13.12 Å2 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.024 / Rrim(I) all: 0.063 / Χ2: 1.077 / Net I/σ(I): 10.3 / Num. measured all: 65939
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.58-1.648.20.1218390.9910.0460.130.78599.5
1.64-1.780.1078410.9940.0420.1160.90199.9
1.7-1.787.90.0938420.9950.0360.10.91699.8
1.78-1.877.70.0878670.9950.0350.0941.05699.9
1.87-1.997.60.0798750.9950.0310.0851.15599.8
1.99-2.147.50.0738540.9940.0290.0781.22899.9
2.14-2.367.60.0658560.9970.0250.071.183100
2.36-2.77.70.0618990.9970.0230.0651.244100
2.7-3.47.30.0558890.9980.0220.0591.212100
3.4-306.30.0479610.9970.0210.0521.11196.9

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Processing

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

Resolution: 1.58→25.18 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.43 / Phase error: 18.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1928 850 9.82 %
Rwork0.1597 7809 -
obs0.1628 8659 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 50.51 Å2 / Biso mean: 19.0997 Å2 / Biso min: 8.57 Å2
Refinement stepCycle: final / Resolution: 1.58→25.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms560 0 3 72 635
Biso mean--12.91 29.82 -
Num. residues----73
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.58-1.680.17211370.14151249138699
1.68-1.810.20361370.128612541391100
1.81-1.990.18011450.167113161461100
1.99-2.280.17661360.153712861422100
2.28-2.870.20381430.18213201463100
2.88-25.180.19851520.15791384153698

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