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7q40

Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2

Method: X-RAY DIFFRACTION Dmax: 103.8 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

E3 ubiquitin-protein ligase HERC2

Homo sapiens

UniProt O95714

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 2938–3342 Not recorded CIT CITRIC ACID × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；hanging drop 20% PEG 3350 0.18M tris amonium citrate Resolution 2.35 Å R-free 0.230
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain C； UniProt 2938–3342 Not recorded CIT CITRIC ACID × 3 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；hanging drop 20% PEG 3350 0.18M tris amonium citrate Resolution 2.35 Å R-free 0.230
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain E； UniProt 2938–3342 Not recorded CIT CITRIC ACID × 4 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；hanging drop 20% PEG 3350 0.18M tris amonium citrate Resolution 2.35 Å R-free 0.230

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 7Q40 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2KEO Solution NMR structure of human protein HS00059, cytochrome-b5-like domain of the HERC2 E3 ligase. Northeast structural genomics consortium (NESG) target ht98a Deposited 2009-01-30 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1203–1296（94 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 300；Pressure ambient
NMR sample composition 0.5 mM [U-13C; U-15N] hs00059-1, 10 mM TRIS-2, 300 mM sodium chloride-3, 10 uM ZnSO4-4, 10 mM DTT-5, 0.01 % NaN3-6, 10 mM benzamidine-7, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
3KCI The third RLD domain of HERC2 Deposited 2009-10-21 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 3951–4321（371 aa） Fragment：UNP RESIDUES 3951-4321, RCC1-LIKE DOMAIN
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；290.9 K；20% PEG3350, 0.2mM MgCl2, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 290.9K
Resolution 1.80 Å R-free 0.195
4L1M Structure of the first RCC1-like domain of HERC2 Deposited 2013-06-03 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 417–790（374 aa）
Not recorded SO4 SULFATE ION × 4 UNX UNKNOWN LIGAND × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；291 K；1.5 M ammonium sulfate, 0.1 M Tris-hydrochloride, pH 8.5, vapor diffusion, temperature 291K
Resolution 2.60 Å R-free 0.238
4L1M Structure of the first RCC1-like domain of HERC2 Deposited 2013-06-03 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 417–790（374 aa）
Not recorded SO4 SULFATE ION × 4 UNX UNKNOWN LIGAND × 12 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；291 K；1.5 M ammonium sulfate, 0.1 M Tris-hydrochloride, pH 8.5, vapor diffusion, temperature 291K
Resolution 2.60 Å R-free 0.238
4L1M Structure of the first RCC1-like domain of HERC2 Deposited 2013-06-03 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 417–790（374 aa）
Not recorded SO4 SULFATE ION × 3 UNX UNKNOWN LIGAND × 13 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；291 K；1.5 M ammonium sulfate, 0.1 M Tris-hydrochloride, pH 8.5, vapor diffusion, temperature 291K
Resolution 2.60 Å R-free 0.238
6WW3 Crystal structure of HERC2 ZZ domain in complex with SUMO1 tail Deposited 2020-05-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2702–2755（54 aa） Fragment：fusion protein
Not recorded ZN ZINC ION × 2 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.2 M ammonium chloride, 0.1 M Tris, pH 8.0 and 20% PEG 6000
Resolution 2.10 Å R-free 0.227
6WW3 Crystal structure of HERC2 ZZ domain in complex with SUMO1 tail Deposited 2020-05-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 2702–2755（54 aa） Fragment：fusion protein
Not recorded ZN ZINC ION × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.2 M ammonium chloride, 0.1 M Tris, pH 8.0 and 20% PEG 6000
Resolution 2.10 Å R-free 0.227
6WW4 Crystal structure of HERC2 ZZ domain in complex with histone H3 tail Deposited 2020-05-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 2702–2751（50 aa） Fragment：fusion protein
Not recorded ZN ZINC ION × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.1 M ammonium acetate, 0.1 M Bis-Tris, pH 5.5, and 17% PEG 10000
Resolution 2.25 Å R-free 0.243
6WW4 Crystal structure of HERC2 ZZ domain in complex with histone H3 tail Deposited 2020-05-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2702–2751（50 aa） Fragment：fusion protein
Not recorded ZN ZINC ION × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.1 M ammonium acetate, 0.1 M Bis-Tris, pH 5.5, and 17% PEG 10000
Resolution 2.25 Å R-free 0.243
7Q41 Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of ubiquitin-protein ligase E3A (E6AP) Deposited 2021-10-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 2938–3342（405 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；293.1500 hanging drop 20% PEG 3350 0.18M tris amonium citrate
Resolution 3.01 Å R-free 0.255
7Q41 Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of ubiquitin-protein ligase E3A (E6AP) Deposited 2021-10-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 2938–3342（405 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；293.1500 hanging drop 20% PEG 3350 0.18M tris amonium citrate
Resolution 3.01 Å R-free 0.255
7Q41 Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of ubiquitin-protein ligase E3A (E6AP) Deposited 2021-10-29 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 2938–3342（405 aa）
Not recorded CIT CITRIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；293.1500 hanging drop 20% PEG 3350 0.18M tris amonium citrate
Resolution 3.01 Å R-free 0.255
7Q42 Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of chromatin reader BAZ2B Deposited 2021-10-29 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 2938–3342（405 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；hanging drop 20% PEG 3350 0.18M tris amonium citrate
Resolution 1.95 Å R-free 0.206
7Q42 Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of chromatin reader BAZ2B Deposited 2021-10-29 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 2938–3342（405 aa）
Not recorded CIT CITRIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；hanging drop 20% PEG 3350 0.18M tris amonium citrate
Resolution 1.95 Å R-free 0.206
7Q42 Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of chromatin reader BAZ2B Deposited 2021-10-29 Different oligomeric state Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 2938–3342（405 aa）
Not recorded CIT CITRIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；hanging drop 20% PEG 3350 0.18M tris amonium citrate
Resolution 1.95 Å R-free 0.206
7Q43 Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of dedicator of cytokinesis protein 10 Deposited 2021-10-29 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 2941–3342（402 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；hanging drop 20% PEG 3350 0.18M tris amonium citrate
Resolution 2.40 Å R-free 0.265
7Q43 Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of dedicator of cytokinesis protein 10 Deposited 2021-10-29 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 2941–3342（402 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；hanging drop 20% PEG 3350 0.18M tris amonium citrate
Resolution 2.40 Å R-free 0.265
7Q43 Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of dedicator of cytokinesis protein 10 Deposited 2021-10-29 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 2941–3342（402 aa）
Not recorded CIT CITRIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；hanging drop 20% PEG 3350 0.18M tris amonium citrate
Resolution 2.40 Å R-free 0.265
7Q44 Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of deubiquitinase USP35 Deposited 2021-10-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 2941–3342（402 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；20% PEG 3350 0.18M tris amonium citrate
Resolution 2.20 Å R-free 0.231
7Q44 Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of deubiquitinase USP35 Deposited 2021-10-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 2941–3342（402 aa）
Not recorded CIT CITRIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；20% PEG 3350 0.18M tris amonium citrate
Resolution 2.20 Å R-free 0.231
7Q44 Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of deubiquitinase USP35 Deposited 2021-10-29 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 2941–3342（402 aa）
Not recorded CIT CITRIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；20% PEG 3350 0.18M tris amonium citrate
Resolution 2.20 Å R-free 0.231
7Q45 Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of Myelin transcription factor 1 Deposited 2021-10-29 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 2938–3342（405 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8；293.15 K；hanging drop 20% PEG 3350 0.18M tris amonium citrate
Resolution 2.10 Å R-free 0.224
7Q45 Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of Myelin transcription factor 1 Deposited 2021-10-29 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 2938–3342（405 aa）
Not recorded CIT CITRIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8；293.15 K；hanging drop 20% PEG 3350 0.18M tris amonium citrate
Resolution 2.10 Å R-free 0.224
7Q45 Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of Myelin transcription factor 1 Deposited 2021-10-29 Different oligomeric state Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 2938–3342（405 aa）
Not recorded CIT CITRIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8；293.15 K；hanging drop 20% PEG 3350 0.18M tris amonium citrate
Resolution 2.10 Å R-free 0.224
7Q46 Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of pericentriolar material 1 protein Deposited 2021-10-29 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 2941–3342（402 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；hanging drop 20% PEG 3350 0.18M tris amonium citrate
Resolution 2.46 Å R-free 0.245
7Q46 Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of pericentriolar material 1 protein Deposited 2021-10-29 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 2941–3342（402 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；hanging drop 20% PEG 3350 0.18M tris amonium citrate
Resolution 2.46 Å R-free 0.245
7Q46 Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of pericentriolar material 1 protein Deposited 2021-10-29 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 2941–3342（402 aa）
Not recorded CIT CITRIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；hanging drop 20% PEG 3350 0.18M tris amonium citrate
Resolution 2.46 Å R-free 0.245
7RGW Crystal structure of HERC2 DOC domain Deposited 2021-07-15 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2759–2914（156 aa） Fragment：DOC domain (UNP residues 2759-2914)
Not recorded PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；0.1 M HEPES, pH 7.5, 25% PEG3350
Resolution 1.99 Å R-free 0.213
9L8Y Crystal structure of HERC2 Deposited 2024-12-28 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2539–2700（162 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.8；289 K；0.02 M Citric acid, 0.08 M BIS-TRIS propane (pH 8.8), 16% w/v Polyethylene glycol 3,350
Resolution 1.92 Å R-free 0.206
9L93 Crystal structure of NCOA4 in complex with HERC2 Deposited 2024-12-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 2539–2700（162 aa）
Not recorded FES FE2/S2 (INORGANIC) CLUSTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；289 K；18% v/v 2-Propanol, 0.1 M Sodium citrate tribasic dihydrate (pH 5.5), 20% w/v Polyethylene glycol 4000
Resolution 1.73 Å R-free 0.207
9L93 Crystal structure of NCOA4 in complex with HERC2 Deposited 2024-12-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2539–2700（162 aa）
Not recorded FES FE2/S2 (INORGANIC) CLUSTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；289 K；18% v/v 2-Propanol, 0.1 M Sodium citrate tribasic dihydrate (pH 5.5), 20% w/v Polyethylene glycol 4000
Resolution 1.73 Å R-free 0.207

14 other PDB entries and 31 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name HERC2_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–405； UniProt 2938–3342 Author chain C； PDBConstruct 1–405； UniProt 2938–3342 Author chain E； PDBConstruct 1–405； UniProt 2938–3342

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 7q40

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7q40
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7q40
Deposition date deposition_date2021-10-29
Structure title titleCrystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2
Keywords keywords7-bladed beta-propeller HERC2 RCC1-like Domain 2 RLD2 ubiquitin ligase DXDKDED motif, PROTEIN BINDING; PROTEIN BINDING
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier34.19 Å
Radius of gyration Rg (electron density) rg_electron33.93 Å
Forward intensity I(0) i0230437000.00
Molecular weight molecular_weight119020.0 kDa
Excluded volume excluded_volume147780 ų
Envelope volume envelope_volume178630 ų
Hydration-shell volume shell_volume43423 ų
Envelope diameter envelope_diameter107.5 Å
Shell Rg shell_rg40.72 Å
Envelope Rg envelope_rg33.78 Å
Shape Rg shape_rg33.89 Å
Total Rg total_rg34.51 Å
Total atoms total_atoms8411
Residues n_residues1108
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax103.8 Å
Rg (real space) rg_real34.09 Å
Rg uncertainty (real space) rg_real_error0.65 Å
I(0) (real space) i0_real2.3040e+08
I(0) uncertainty (real space) i0_real_error3.3780e+06
Rg (reciprocal space) rg_reciprocal34.15 Å
I(0) (reciprocal space) i0_reciprocal230400000.0000
Solution quality estimate total_estimate0.9016
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary33.9 Å
Skewness Skewness skewness0.129
Kurtosis Kurtosis kurtosis-0.758
Angular range angular_range— – 0.2300 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha55640000.0000
Real-space data points n_real_points47
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.966; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.818
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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8. Citations (1)

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9. Files and Curves (10)