SAXSdb — 2gyt

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

Deleted in liver cancer 1 protein, isoform 2

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 1–76	Fragment：sterile alpha motif (SAM) domain	No other associated polymer	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

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 2GYT	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2DKY Solution structure of the SAM-domain of Rho-GTPase-activating protein 7 Deposited 2006-04-14	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–78（78 aa） Fragment：SAM-domain	Not recorded	No recorded non-water small molecule	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
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 1–76； UniProt 1–76

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	2gyt
Deposition date deposition_date	2006-05-10
Structure title title	Solution structure of the SAM (sterile alpha motif) domain of DLC1 (deleted in liver cancer 1)
Keywords keywords	SAM domain, protein structure, PROTEIN BINDING; PROTEIN BINDING
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	14.01 Å
Radius of gyration Rg (electron density) rg_electron	13.75 Å
Forward intensity I(0) i0	114620000.00
Molecular weight molecular_weight	89525.0 kDa
Excluded volume excluded_volume	112370 Å³
Envelope volume envelope_volume	24382 Å³
Hydration-shell volume shell_volume	13091 Å³
Envelope diameter envelope_diameter	62.9 Å
Shell Rg shell_rg	21.97 Å
Envelope Rg envelope_rg	17.68 Å
Shape Rg shape_rg	13.65 Å
Total Rg total_rg	14.45 Å
Total atoms total_atoms	11490
Residues n_residues	760
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	57.9 Å
Rg (real space) rg_real	14.13 Å
Rg uncertainty (real space) rg_real_error	0.68 Å
I(0) (real space) i0_real	1.1460e+08
I(0) uncertainty (real space) i0_real_error	1.6550e+06
Rg (reciprocal space) rg_reciprocal	14.12 Å
I(0) (reciprocal space) i0_reciprocal	114600000.0000
Solution quality estimate total_estimate	0.7201
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	16.1 Å
Skewness Skewness skewness	0.613
Kurtosis Kurtosis kurtosis	0.413
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	139500.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.299; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.461; Smooth: 0.999

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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

SCOP 2.08 (1 domains)

Domain ID domain_id	d2gyta1
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

CATH v4.4 (1 domains)

Domain ID domain_id	2gytA01
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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Description description	Deleted in liver cancer 1 protein, isoform 2
Molecular weight formula_weight	8965.5 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	11490

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21(DE3)

fit	/app/data/saxs_computation/gy/2gyt/2gyt.fit
pddf	/app/data/pr_computation/gy/2gyt/2gyt.pr.out
profile	/app/data/saxs_computation/gy/2gyt/2gyt.dat

Solution structure of the SAM (sterile alpha motif) domain of DLC1 (deleted in liver cancer 1)

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

Deleted in liver cancer 1 protein, isoform 2

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)