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8ux2

Chromobacterium violaceum mono-ADP-ribosyltransferase CteC in complex with NAD+

Method: X-RAY DIFFRACTION Dmax: 106.1 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

NAD(+)--protein-threonine ADP-ribosyltransferase

Chromobacterium violaceum

UniProt Q7NY09

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 36–276 Non-standard monomer：Yes (specific site not provided by mmCIF) NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 CA CALCIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.25M calcium acetate, 20% PEG 3000 Resolution 1.87 Å R-free 0.227
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 36–276 Non-standard monomer：Yes (specific site not provided by mmCIF) NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 CA CALCIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.25M calcium acetate, 20% PEG 3000 Resolution 1.87 Å R-free 0.227
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain C； UniProt 36–276 Non-standard monomer：Yes (specific site not provided by mmCIF) NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 CA CALCIUM ION × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.25M calcium acetate, 20% PEG 3000 Resolution 1.87 Å R-free 0.227

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 8UX2 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
8HTC Crystal structure of a SeMet-labeled effector from Chromobacterium violaceum in complex with Ubiquitin Deposited 2022-12-21 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 45–276（232 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.25；289 K；100 mM sodium cacodylate, pH 6.25, 200 mM sodium acetate, 22% PEG 8000
Resolution 2.20 Å R-free 0.247
8HTD Crystal structure of an effector from Chromobacterium violaceum in complex with ubiquitin Deposited 2022-12-21 Different construct Different mutation/modification 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 45–276（232 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；100 mM sodium cacodylate, pH 6.5, 200 mM sodium acetate, 28% to 30% PEG 8000
Resolution 1.85 Å R-free 0.225
8HTE Crystal structure of an effector mutant in complex with ubiquitin Deposited 2022-12-21 Different construct Different mutation/modification 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 45–276（232 aa）
Mutation：E220A SO4 SULFATE ION × 2 GOL GLYCEROL × 2 NCA NICOTINAMIDE × 1 AR6 [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；289 K；100 mM BIS-TRIS propane, pH 7.0, and 1.5 M ammonium sulfate
Resolution 2.31 Å R-free 0.228
8HTF Crystal structure of an effector in complex with ubiquitin Deposited 2022-12-21 Different construct Different mutation/modification 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 45–276（232 aa）
Not recorded NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.25；289 K；100 mM sodium cacodylate, pH 6.25, 200 mM sodium acetate, 22% PEG 8000, 25% glycerol
Resolution 2.15 Å R-free 0.223

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CTEC_CHRVO
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 6–246； UniProt 36–276 Author chain B； PDBConstruct 6–246； UniProt 36–276 Author chain C； PDBConstruct 6–246； UniProt 36–276

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 8ux2

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8ux2
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8ux2
Deposition date deposition_date2023-11-08
Structure title titleChromobacterium violaceum mono-ADP-ribosyltransferase CteC in complex with NAD+
Keywords keywordsmono-ADP-ribosyltransferase, ADP-ribosylation, bacterial effector, TRANSFERASE; TRANSFERASE
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_guinier32.88 Å
Radius of gyration Rg (electron density) rg_electron32.45 Å
Forward intensity I(0) i0116052000.00
Molecular weight molecular_weight80583.0 kDa
Excluded volume excluded_volume98108 ų
Envelope volume envelope_volume128280 ų
Hydration-shell volume shell_volume33804 ų
Envelope diameter envelope_diameter114.5 Å
Shell Rg shell_rg38.24 Å
Envelope Rg envelope_rg31.93 Å
Shape Rg shape_rg32.46 Å
Total Rg total_rg32.89 Å
Total atoms total_atoms5592
Residues n_residues694
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 dmax106.1 Å
Rg (real space) rg_real32.91 Å
Rg uncertainty (real space) rg_real_error1.09 Å
I(0) (real space) i0_real1.1610e+08
I(0) uncertainty (real space) i0_real_error2.0320e+06
Rg (reciprocal space) rg_reciprocal32.91 Å
I(0) (reciprocal space) i0_reciprocal116100000.0000
Solution quality estimate total_estimate0.8970
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary30.9 Å
Skewness Skewness skewness0.260
Kurtosis Kurtosis kurtosis-0.636
Angular range angular_range— – 0.2400 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha18780000.0000
Real-space data points n_real_points49
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.936; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.943; Smooth: 0.907
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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8. Citations (1)

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9. Files and Curves (10)