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- PDB-7wum: Crystal structure of UBR box from PRT6 (RDG pH 8.5) -

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Basic information

Entry
Database: PDB / ID: 7wum
TitleCrystal structure of UBR box from PRT6 (RDG pH 8.5)
Components
  • 3-mer peptide
  • E3 ubiquitin-protein ligase
KeywordsLIGASE / E3 ligase / PRT6 UBR box
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, C.C.
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
Water73941
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 area4210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.756, 29.756, 115.566
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: 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 / Water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 31.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1M sodium citrate, 200mM NaCl and 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 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.58→50 Å / Num. obs: 8791 / % possible obs: 98.2 % / Redundancy: 7.7 % / Biso Wilson estimate: 19.51 Å2 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.031 / Rrim(I) all: 0.082 / Χ2: 1.635 / Net I/σ(I): 8.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.58-1.613.80.3212920.9640.1580.3610.7969.7
1.61-1.644.30.3124340.9860.1430.3460.86798.2
1.64-1.675.20.3024400.9790.1340.3320.848100
1.67-1.76.30.2774110.9840.1180.3020.873100
1.7-1.747.10.2924650.9790.1160.3150.917100
1.74-1.788.40.2654140.9870.0990.2830.88599.8
1.78-1.828.70.2584250.9910.0950.2760.906100
1.82-1.879.10.2244700.9920.0810.2390.95899.8
1.87-1.939.30.24200.990.0710.2131.048100
1.93-1.999.20.1864410.990.0670.1981.24599.5
1.99-2.0690.154240.9920.0550.161.334100
2.06-2.149.10.1394600.9920.0510.1481.501100
2.14-2.248.80.1164230.9930.0430.1241.71399.8
2.24-2.368.70.1064630.9950.040.1141.851100
2.36-2.5190.0954430.9940.0360.1012.00699.6
2.51-2.78.60.0924540.9960.0350.0992.49299.8
2.7-2.978.20.0794540.9970.030.0852.65699.6
2.97-3.47.50.0664570.9970.0270.0722.854100
3.4-4.296.60.0534840.9970.0230.0582.91799.6
4.29-5060.0535170.9960.0240.0583.00997.5

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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→25.77 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 29.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2105 875 10.03 %
Rwork0.1789 7848 -
obs0.1822 8723 98.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 62.56 Å2 / Biso mean: 28.4289 Å2 / Biso min: 14.86 Å2
Refinement stepCycle: final / Resolution: 1.58→25.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms560 0 3 41 604
Biso mean--21.89 35.67 -
Num. residues----73
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.58-1.670.26841330.2046118793
1.67-1.80.23541430.1554127799
1.8-1.980.20491450.2016131899
1.98-2.270.20731500.18181294100
2.27-2.860.23141460.19531338100
2.86-25.770.19671580.1684143499

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