SAXSdb — 1lxd

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

RALGDSB

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 694–864 Chain B； UniProt 694–864	Fragment：C-TERMINAL DOMAIN WHICH BINDS TO ACTIVE RAS Mutation：N-TERMINAL GS INHERITED FROM THE LINKER SEQUENCE OF THE CLONING VECTOR	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8.5；PROTEIN WAS CRYSTALLIZED FROM 20% PEG 8000, 0.1 M TRIS PH 8.5, AND 0.2 M CALCIUM ACETATE.	Resolution 2.40 Å R-free 0.298

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 1LXD	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1LFD CRYSTAL STRUCTURE OF THE ACTIVE RAS PROTEIN COMPLEXED WITH THE RAS-INTERACTING DOMAIN OF RALGDS Deposited 1998-04-29	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 778–864（87 aa） Fragment：RAS-INTERACTING DOMAIN, C-TERMINAL DOMAIN	Not recorded	MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 2.10 Å R-free 0.282
1LFD CRYSTAL STRUCTURE OF THE ACTIVE RAS PROTEIN COMPLEXED WITH THE RAS-INTERACTING DOMAIN OF RALGDS Deposited 1998-04-29	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 778–864（87 aa） Fragment：RAS-INTERACTING DOMAIN, C-TERMINAL DOMAIN	Not recorded	MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 2.10 Å R-free 0.282

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

View Construct and Data Evidence

UniProt name	GNDS_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–100； UniProt 694–864 Author chain B； PDBConstruct 1–100； UniProt 694–864

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	1lxd
Deposition date deposition_date	1997-03-05
Structure title title	CRYSTAL STRUCTURE OF THE RAS INTERACTING DOMAIN OF RALGDS, A GUANINE NUCLEOTIDE DISSOCIATION STIMULATOR OF RAL PROTEIN
Keywords keywords	PHOSPHORYLATION, RALGDS, RAS BINDING, UBIQUITIN FOLD, CDC25 FAMILY, SIGNAL TRANSDUCTION, CROSS-TALK; PHOSPHORYLATION
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	20.82 Å
Radius of gyration Rg (electron density) rg_electron	19.84 Å
Forward intensity I(0) i0	7485920.00
Molecular weight molecular_weight	19909.0 kDa
Excluded volume excluded_volume	24767 Å³
Envelope volume envelope_volume	30735 Å³
Hydration-shell volume shell_volume	13739 Å³
Envelope diameter envelope_diameter	65.4 Å
Shell Rg shell_rg	24.65 Å
Envelope Rg envelope_rg	20.22 Å
Shape Rg shape_rg	19.88 Å
Total Rg total_rg	20.47 Å
Total atoms total_atoms	1704
Residues n_residues	174
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	66.2 Å
Rg (real space) rg_real	20.94 Å
Rg uncertainty (real space) rg_real_error	0.39 Å
I(0) (real space) i0_real	7.4860e+06
I(0) uncertainty (real space) i0_real_error	1.0550e+05
Rg (reciprocal space) rg_reciprocal	20.92 Å
I(0) (reciprocal space) i0_reciprocal	7486000.0000
Solution quality estimate total_estimate	0.8711
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	64.2 Å
Skewness Skewness skewness	0.389
Kurtosis Kurtosis kurtosis	-0.635
Angular range angular_range	— – 0.3800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2213000.0000
Real-space data points n_real_points	70
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.820; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.870; Smooth: 0.991

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1lxda_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.5 — Ras-binding domain, RBD

Domain ID domain_id	d1lxdb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.5 — Ras-binding domain, RBD

CATH v4.4 (2 domains)

Domain ID domain_id	1lxdA00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Domain ID domain_id	1lxdB00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

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8. Citations (3)

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Unit-cell length a length_a	105.282 Å
Unit-cell length b length_b	30.714 Å
Unit-cell length c length_c	51.326 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	94.57 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	6.000 Å
R factor r_factor	0.2120
R_work r_work	0.2120
R_free r_free	0.2980

Description description	RALGDSB
Molecular weight formula_weight	11350.8 kDa
Mutation mutation	N-TERMINAL GS INHERITED FROM THE LINKER SEQUENCE OF THE CLONING VECTOR
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1878

CRYSTAL STRUCTURE OF THE RAS INTERACTING DOMAIN OF RALGDS, A GUANINE NUCLEOTIDE DISSOCIATION STIMULATOR OF RAL PROTEIN

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

RALGDSB

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (3)

9. Files and Curves (10)

Files (7)

Curves (3)

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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	58

fit	/app/data/saxs_computation/lx/1lxd/1lxd.fit
pddf	/app/data/pr_computation/lx/1lxd/1lxd.pr.out
profile	/app/data/saxs_computation/lx/1lxd/1lxd.dat