← Back to search
4mt6

Crystal structure of closed inactive collybistin

Method: X-RAY DIFFRACTION Dmax: 86.9 Å Quality: EXCELLENT
▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

Rho guanine nucleotide exchange factor 9

Rattus norvegicus

UniProt Q9QX73

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 1–456 Mutation：G33E, V34L No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；20mM Na-cacodylate, 5mM Co(III)hexamine chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 5.50 Å R-free 0.282

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 4MT6 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2DFK Crystal structure of the CDC42-Collybistin II complex Deposited 2006-03-02 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 10–411（402 aa） Fragment：residues 10-411
Not recorded GOL GLYCEROL × 4 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；PEG 8000, Potassium dihydrogen phosphate, NaCl, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K, pH 8.00
Resolution 2.15 Å R-free 0.229
2DFK Crystal structure of the CDC42-Collybistin II complex Deposited 2006-03-02 Different construct Different mutation/modification 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 10–411（402 aa） Fragment：residues 10-411
Not recorded GOL GLYCEROL × 2 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；PEG 8000, Potassium dihydrogen phosphate, NaCl, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K, pH 8.00
Resolution 2.15 Å R-free 0.229
2DFK Crystal structure of the CDC42-Collybistin II complex Deposited 2006-03-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 10–411（402 aa） Fragment：residues 10-411
Chain C 10–411（402 aa） Fragment：residues 10-411
Not recorded GOL GLYCEROL × 6 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；PEG 8000, Potassium dihydrogen phosphate, NaCl, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K, pH 8.00
Resolution 2.15 Å R-free 0.229
4MT7 Crystal structure of collybistin I Deposited 2013-09-19 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 10–493（484 aa） Fragment：unp residues 10-493
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；100mM MES, 15% PEG 20000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.50 Å R-free 0.249

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

View Construct and Data Evidence
UniProt name ARHG9_RAT
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–456； UniProt 1–456

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 4mt6

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4mt6
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id4mt6
Deposition date deposition_date2013-09-19
Structure title titleCrystal structure of closed inactive collybistin
Keywords keywordsclosed conformation, PROTEIN BINDING; PROTEIN BINDING
Experimental Method methodX-RAY DIFFRACTION
▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier27.19 Å
Radius of gyration Rg (electron density) rg_electron26.26 Å
Forward intensity I(0) i037647600.00
Molecular weight molecular_weight46750.0 kDa
Excluded volume excluded_volume58261 ų
Envelope volume envelope_volume75928 ų
Hydration-shell volume shell_volume25453 ų
Envelope diameter envelope_diameter90.5 Å
Shell Rg shell_rg32.10 Å
Envelope Rg envelope_rg25.92 Å
Shape Rg shape_rg26.25 Å
Total Rg total_rg26.98 Å
Total atoms total_atoms3292
Residues n_residues389
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
▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax86.9 Å
Rg (real space) rg_real27.23 Å
Rg uncertainty (real space) rg_real_error0.53 Å
I(0) (real space) i0_real3.7650e+07
I(0) uncertainty (real space) i0_real_error4.8220e+05
Rg (reciprocal space) rg_reciprocal27.22 Å
I(0) (reciprocal space) i0_reciprocal37650000.0000
Solution quality estimate total_estimate0.9039
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary28.5 Å
Skewness Skewness skewness0.321
Kurtosis Kurtosis kurtosis-0.514
Angular range angular_range— – 0.2900 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5611000.0000
Real-space data points n_real_points59
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.944; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.938
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (1)

▶

8. Citations (1)

▶

9. Files and Curves (10)