SAXSdb — 4mt7

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

Rho guanine nucleotide exchange factor 9

Rattus norvegicus

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 10–493	Fragment：unp residues 10-493	No other associated polymer	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

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 4MT7	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 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 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
4MT6 Crystal structure of closed inactive collybistin 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 1–456（456 aa）	Mutation：G33E, V34L	No recorded non-water small molecule	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

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 1–484； UniProt 10–493

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4mt7
Deposition date deposition_date	2013-09-19
Structure title title	Crystal structure of collybistin I
Keywords keywords	extended conformation, PROTEIN BINDING; PROTEIN BINDING
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	28.99 Å
Radius of gyration Rg (electron density) rg_electron	28.31 Å
Forward intensity I(0) i0	28492400.00
Molecular weight molecular_weight	40678.0 kDa
Excluded volume excluded_volume	50649 Å³
Envelope volume envelope_volume	66420 Å³
Hydration-shell volume shell_volume	20720 Å³
Envelope diameter envelope_diameter	96.0 Å
Shell Rg shell_rg	33.62 Å
Envelope Rg envelope_rg	27.98 Å
Shape Rg shape_rg	28.31 Å
Total Rg total_rg	28.87 Å
Total atoms total_atoms	2859
Residues n_residues	337
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	90.5 Å
Rg (real space) rg_real	29.11 Å
Rg uncertainty (real space) rg_real_error	0.68 Å
I(0) (real space) i0_real	2.8490e+07
I(0) uncertainty (real space) i0_real_error	4.1520e+05
Rg (reciprocal space) rg_reciprocal	29.07 Å
I(0) (reciprocal space) i0_reciprocal	28490000.0000
Solution quality estimate total_estimate	0.8714
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.0 Å
Skewness Skewness skewness	0.293
Kurtosis Kurtosis kurtosis	-0.782
Angular range angular_range	— – 0.2750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5011000.0000
Real-space data points n_real_points	56
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.900; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.727; Smooth: 0.898

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	4mt7A01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	900 — Dbl Homology Domain; Chain A
Homologous superfamily homologous superfamily	10 — Dbl homology (DH) domain

Domain ID domain_id	4mt7A02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	29 — PH-domain like
Homologous superfamily homologous superfamily	30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)

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8. Citations (1)

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Unit-cell length a length_a	82.930 Å
Unit-cell length b length_b	165.430 Å
Unit-cell length c length_c	129.120 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	3.500 Å
Low-resolution limit resolution_low	50.893 Å
R factor r_factor	0.2228
R_work r_work	0.2207
R_free r_free	0.2487

Description description	Rho guanine nucleotide exchange factor 9
Molecular weight formula_weight	57368.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2859

Crystal structure of collybistin I

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

Rho guanine nucleotide exchange factor 9

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Rattus norvegicus
通用名 common_name	rat
NCBI Class编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Escherichia coli

fit	/app/data/saxs_computation/mt/4mt7/4mt7.fit
pddf	/app/data/pr_computation/mt/4mt7/4mt7.pr.out
profile	/app/data/saxs_computation/mt/4mt7/4mt7.dat