SAXSdb — 2df6

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

Rho guanine nucleotide exchange factor 7

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 10–63	Fragment：SH3 domain(residues 10-63)	18-mer from PAK2 × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.7；277 K；100mM MES, 35% PEG 5000MME, 200mM ammonium sulfate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.30 Å R-free 0.215
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 10–63	Fragment：SH3 domain(residues 10-63)	18-mer from PAK2 × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.7；277 K；100mM MES, 35% PEG 5000MME, 200mM ammonium sulfate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.30 Å R-free 0.215

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 2DF6	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2AK5 beta PIX-SH3 complexed with a Cbl-b peptide Deposited 2005-08-03	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 5–66（62 aa） Fragment：beta-pix SH3A Chain B 5–66（62 aa） Fragment：beta-pix SH3A	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；291 K；PEG 3000, SODIUM CITRATE, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K, pH 6.50	Resolution 1.85 Å R-free 0.269
2G6F Crystal Structure of the SH3 Domain of betaPIX in Complex with a High Affinity Peptide from PAK2 Deposited 2006-02-24	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain X 10–63（54 aa） Fragment：SH3 domain(residues 10-63)	Not recorded	NCO COBALT HEXAMMINE(III) × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；0.1M HEPES, 53% MPD, 200mM [Co(NH3)]Cl3, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 0.92 Å R-free 0.199
2P4R Structural basis for a novel interaction between AIP4 and beta-PIX Deposited 2007-03-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 10–63（54 aa） Fragment：Beta-PIX SH3 (10-63)	Not recorded	SO4 SULFATE ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M TrisHCl, 0.2 M ammonium sulfate, 32-38% (w/v) PEG-MME 5000, pH 7.1-7.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.246
2P4R Structural basis for a novel interaction between AIP4 and beta-PIX Deposited 2007-03-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 10–63（54 aa） Fragment：Beta-PIX SH3 (10-63)	Not recorded	SO4 SULFATE ION × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M TrisHCl, 0.2 M ammonium sulfate, 32-38% (w/v) PEG-MME 5000, pH 7.1-7.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.246
2W6B Crystal Structure of the Trimeric beta-PIX Coiled-Coil Domain Deposited 2008-12-17	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 588–638（51 aa） Fragment：COILED-COIL, RESIDUES 588-638	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 35% MPD, 0.24 M NON-DETERGENT SULPHOBETAINE 195 (NDSB-195)	Resolution 2.80 Å R-free 0.305
3L4F Crystal Structure of betaPIX Coiled-Coil Domain and Shank PDZ Complex Deposited 2009-12-19	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 587–646（60 aa） Fragment：The C-terminal coiled-coil domain Chain B 587–646（60 aa） Fragment：The C-terminal coiled-coil domain Chain C 587–646（60 aa） Fragment：The C-terminal coiled-coil domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；15% ETHANOL, 10% ETHYLENE GLYCOL, 0.1M MES-NAOH, pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.80 Å R-free 0.307

5 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ARHG7_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–59； UniProt 10–63 Author chain B； PDBConstruct 6–59； UniProt 10–63

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	2df6
Deposition date deposition_date	2006-02-25
Structure title title	Crystal Structure of the SH3 Domain of betaPIX in Complex with a High Affinity Peptide from PAK2
Keywords keywords	SH3 domain, Peptide interaction, SIGNALING PROTEIN; SIGNALING PROTEIN
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	17.73 Å
Radius of gyration Rg (electron density) rg_electron	17.15 Å
Forward intensity I(0) i0	5557860.00
Molecular weight molecular_weight	16820.0 kDa
Excluded volume excluded_volume	20846 Å³
Envelope volume envelope_volume	23484 Å³
Hydration-shell volume shell_volume	12228 Å³
Envelope diameter envelope_diameter	59.5 Å
Shell Rg shell_rg	21.82 Å
Envelope Rg envelope_rg	17.42 Å
Shape Rg shape_rg	17.12 Å
Total Rg total_rg	18.04 Å
Total atoms total_atoms	1195
Residues n_residues	148
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	59.4 Å
Rg (real space) rg_real	17.79 Å
Rg uncertainty (real space) rg_real_error	0.50 Å
I(0) (real space) i0_real	5.5580e+06
I(0) uncertainty (real space) i0_real_error	6.8850e+04
Rg (reciprocal space) rg_reciprocal	17.78 Å
I(0) (reciprocal space) i0_reciprocal	5558000.0000
Solution quality estimate total_estimate	0.6582
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	53.1 Å
Skewness Skewness skewness	0.372
Kurtosis Kurtosis kurtosis	-0.506
Angular range angular_range	— – 0.4500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1808000.0000
Real-space data points n_real_points	76
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.815; Stabil: 0.998; Sysdev: 0.424; Positv: 1.000; Valcen: 0.840; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Rho guanine nucleotide exchange factor 7
Molecular weight formula_weight	6731.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1336

GPLGSVVRAKFNFQQTNEDELSFSKGDVIHVTRVEEGGWWEGTHNGRTGWFPSNYVREI

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	Norway rat
NCBI Class编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	18-mer from PAK2
Molecular weight formula_weight	2053.4 kDa
EC 编号 ec_number	2.7.1.37
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

PPVIAPRPEHTKSIYTRS

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	141

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	2df6A00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	40 — SH3 Domains

Domain ID domain_id	2df6B00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	40 — SH3 Domains

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8. Citations (1)

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Unit-cell length a length_a	50.217 Å
Unit-cell length b length_b	50.217 Å
Unit-cell length c length_c	100.317 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 61
Space-group number int_tables_number	169
Crystal system crystal_system	—

Resolution resolution	1.300 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2040
R_work r_work	0.2010
R_free r_free	0.2150

fit	/app/data/saxs_computation/df/2df6/2df6.fit
pddf	/app/data/pr_computation/df/2df6/2df6.pr.out
profile	/app/data/saxs_computation/df/2df6/2df6.dat

Crystal Structure of the SH3 Domain of betaPIX in Complex with a High Affinity Peptide from PAK2

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

Rho guanine nucleotide exchange factor 7

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)