SAXSdb — 2dky

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

Rho-GTPase-activating protein 7

Homo sapiens

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 1–78	Fragment：SAM-domain	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 7；296 K；Ionic strength (raw mmCIF value) 120mM；Pressure AMBIENT NMR sample composition：1.08mM SAM DOMAIN, 20mM d-TRIS-HCL, 100mM NaCl, 1mM d-DTT, 0.02% NaN3, 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided

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 2DKY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2GYT Solution structure of the SAM (sterile alpha motif) domain of DLC1 (deleted in liver cancer 1) Deposited 2006-05-10	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–76（76 aa） Fragment：sterile alpha motif (SAM) domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 50mM sodium phosphate；Pressure 1 NMR sample composition 1mM DLC1-SAM 15N, 13C-labaled; 50mM sodium phosphate buffer(pH 7.0); 3mM DTT; 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 1mM DLC1-SAM 15N-labaled; 50mM sodium phosphate buffer(pH 7.0); 3mM DTT; 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
2KAP Solution structure of DLC1-SAM Deposited 2008-11-12	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 17–76（60 aa） Fragment：sterile alpha motif (SAM) domain, UNP residues 17-76	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；298 K；Pressure ambient NMR sample composition 1mM DLC1-SAM, 50mM sodium phosphate, 3mM DTT, 5% [U-100% 2H] D2O, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 1mM [U-100% 15N] DLC1-SAM, 50mM sodium phosphate, 3mM DTT, 5% [U-100% 2H] D2O, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 1mM [U-100% 13C; U-100% 15N] DLC1-SAM, 50mM sodium phosphate, 3mM DTT, 5% [U-100% 2H] D2O, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 1mM DLC1-SAM, 50mM sodium phosphate, 3mM DTT, 100 % D2O, 100% D2O \| 100% D2O NMR sample composition 1mM [U-100% 13C; U-100% 15N] DLC1-SAM, 50mM sodium phosphate, 3mM DTT, 100% D2O, 100% D2O \| 100% D2O	Resolution not provided
2LOZ The novel binding mode of DLC1 and Tensin2 PTB domain Deposited 2012-01-29	Different construct Different oligomeric state Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 811–824（14 aa） Fragment：UNP residues 811-824	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 0.2；Pressure ambient NMR sample composition 0.6-0.8 mM [U-100% 13C; U-100% 15N] Tensin2-1, 1.2-1.4 mM DLC1-2, 100 mM potassium phosphate-3, 100 mM potassium chloride-4, 1 mM EDTA-5, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1.2-1.4 mM Tensin2-6, 0.6-0.8 mM [U-100% 13C; U-100% 15N] DLC1-7, 100 mM potassium phosphate-8, 100 mM potassium chloride-9, 1 mM EDTA-10, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.6-0.8 mM [U-100% 13C] Tensin2-11, 1.2-1.4 mM DLC1-12, 100 mM potassium phosphate-13, 100 mM potassium chloride-14, 1 mM EDTA-15, 100% D2O \| 100% D2O NMR sample composition 1.2-1.4 mM Tensin2-16, 0.6-0.8 mM [U-100% 13C] DLC1-17, 100 mM potassium phosphate-18, 100 mM potassium chloride-19, 1 mM EDTA-20, 100% D2O \| 100% D2O	Resolution not provided
3KUQ Crystal structure of the DLC1 RhoGAP domain Deposited 2009-11-27	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 1066–1275（210 aa） Fragment：Rho-GAP domain	Not recorded	UNX UNKNOWN LIGAND × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；291 K；30% PEG-3350, 0.2M sodium chloride, 5% glycerol, 0.02M HEPES, pH 7.5, vapor diffusion, hanging drop, temperature 291K, VAPOR DIFFUSION, HANGING DROP	Resolution 2.30 Å R-free 0.260
5FZT The crystal structure of R7R8 in complex with a DLC1 fragment. Deposited 2016-03-15	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 467–489（23 aa） Fragment：TBS, UNP RESIDUES 467-489	Not recorded	MLI MALONATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.4；15% ETHANOL, 0.1 M TRIS PH 7.4 AT 4OC	Resolution 2.10 Å R-free 0.231

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

View Construct and Data Evidence

UniProt name	RHG07_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 8–85； UniProt 1–78

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	2dky
Deposition date deposition_date	2006-04-14
Structure title title	Solution structure of the SAM-domain of Rho-GTPase-activating protein 7
Keywords keywords	;CELL-FREE PROTEIN SYNTHESIS, PROTEIN REGULATION, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, SIGNALING PROTEIN ;; SIGNALING PROTEIN
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	15.47 Å
Radius of gyration Rg (electron density) rg_electron	14.87 Å
Forward intensity I(0) i0	611453000.00
Molecular weight molecular_weight	203370.0 kDa
Excluded volume excluded_volume	252640 Å³
Envelope volume envelope_volume	43533 Å³
Hydration-shell volume shell_volume	18728 Å³
Envelope diameter envelope_diameter	67.0 Å
Shell Rg shell_rg	25.93 Å
Envelope Rg envelope_rg	20.33 Å
Shape Rg shape_rg	14.81 Å
Total Rg total_rg	15.34 Å
Total atoms total_atoms	28320
Residues n_residues	1820
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	40.7 Å
Rg (real space) rg_real	14.67 Å
Rg uncertainty (real space) rg_real_error	0.05 Å
I(0) (real space) i0_real	5.8310e+08
I(0) uncertainty (real space) i0_real_error	5.0100e+06
Rg (reciprocal space) rg_reciprocal	15.55 Å
I(0) (reciprocal space) i0_reciprocal	611500000.0000
Solution quality estimate total_estimate	0.6823
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	16.0 Å
Skewness Skewness skewness	0.254
Kurtosis Kurtosis kurtosis	-0.499
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	4.7090
Highest regularization parameter α highest_alpha	189100.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.002; Oscil: 0.976; Stabil: 0.981; Sysdev: 0.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

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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) 4 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d2dkya1
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.1 — SAM/Pointed domain
Family Family family	a.60.1.3 — Variant SAM domain

Domain ID domain_id	d2dkya2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2dkya3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id	2dkyA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	2070 —

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	1

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Description description	Rho-GTPase-activating protein 7
Molecular weight formula_weight	10199.7 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	28320

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606

Solution structure of the SAM-domain of Rho-GTPase-activating protein 7

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

Rho-GTPase-activating protein 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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (3 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

fit	/app/data/saxs_computation/dk/2dky/2dky.fit
pddf	/app/data/pr_computation/dk/2dky/2dky.pr.out
profile	/app/data/saxs_computation/dk/2dky/2dky.dat