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- PDB-5w87: Crystal structure of the C-terminal lobe of the human HERC6 HECT ... -

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Basic information

Entry
Database: PDB / ID: 5w87
TitleCrystal structure of the C-terminal lobe of the human HERC6 HECT domain
ComponentsProbable E3 ubiquitin-protein ligase HERC6
KeywordsTRANSFERASE/LIGASE / E3 ligase / antiviral activity / TRANSFERASE-LIGASE complex
Function / homology
Function and homology information


HECT-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / Antigen processing: Ubiquitination & Proteasome degradation / nucleoplasm / cytosol
Similarity search - Function
Regulator of chromosome condensation (RCC1) signature 2. / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation, RCC1 / Regulator of chromosome condensation (RCC1) repeat profile. / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with
Similarity search - Domain/homology
PHOSPHATE ION / Probable E3 ubiquitin-protein ligase HERC6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.199 Å
AuthorsWANG, Y. / BELLESIS, A.G. / ROYER, W.E. / SPRATT, D.E.
Funding support United States, 1items
OrganizationGrant numberCountry
Clark University start-up funds United States
CitationJournal: To Be Published
Title: Crystal structure of the C-terminal lobe of the human HERC6 HECT domain
Authors: WANG, Y. / BELLESIS, A.G. / ROYER, W.E. / SPRATT, D.E.
History
DepositionJun 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
A: Probable E3 ubiquitin-protein ligase HERC6
B: Probable E3 ubiquitin-protein ligase HERC6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8603
Polymers28,7652
Non-polymers951
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-41 kcal/mol
Surface area10270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.579, 74.579, 114.890
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-1101-

PO4

21A-1101-

PO4

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Components

#1: Protein Probable E3 ubiquitin-protein ligase HERC6 / HECT domain and RCC1-like domain-containing protein 6 / HECT-type E3 ubiquitin transferase HERC6


Mass: 14382.314 Da / Num. of mol.: 2 / Fragment: C-terminal lobe (UNP residues 902-1022) / Mutation: C970S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HERC6 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) CodonPlus RIL
References: UniProt: Q8IVU3, HECT-type E3 ubiquitin transferase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.14 Å3/Da / Density % sol: 42.46 % / Description: triangular pyramid with soft vertices
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: K2HPO4/NaH2PO4, NaCl, imidazole:HCl / PH range: 7.6-8.0

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Data collection

DiffractionMean temperature: 298.15 K / Ambient temp details: room temperature
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Mar 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.199→23.88 Å / Num. obs: 11479 / % possible obs: 91.75 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.05707 / Rpim(I) all: 0.0349 / Net I/σ(I): 12.12
Reflection shellResolution: 2.199→2.278 Å / Rmerge(I) obs: 0.7581 / Num. unique obs: 782 / Rpim(I) all: 0.6231 / % possible all: 64.41

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: 000)refinement
HKL-3000data collection
HKL-3000data scaling
PHENIXphasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1C4Z

1c4z


Resolution: 2.199→23.879 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 31.65
RfactorNum. reflection% reflection
Rfree0.2435 557 5.01 %
Rwork0.2112 --
obs0.2129 11127 91.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.199→23.879 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1521 0 5 35 1561
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021564
X-RAY DIFFRACTIONf_angle_d0.5282114
X-RAY DIFFRACTIONf_dihedral_angle_d4.661915
X-RAY DIFFRACTIONf_chiral_restr0.036230
X-RAY DIFFRACTIONf_plane_restr0.003263
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.199-2.420.32611240.29662278X-RAY DIFFRACTION79
2.42-2.76980.32891540.28092858X-RAY DIFFRACTION100
2.7698-3.48790.27391470.22862873X-RAY DIFFRACTION100
3.4879-23.880.19781320.17612561X-RAY DIFFRACTION89

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