SAXSdb — 1gcp

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

VAV PROTO-ONCOGENE

Mus musculus

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 595–660	Fragment：N-TERMINAL DOMAIN	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；277.2 K；PEG4000, tris(hydroxymethyl)aminomethane, isopropanol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.2K	Resolution 2.10 Å R-free 0.253
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 595–660	Fragment：N-TERMINAL DOMAIN	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；277.2 K；PEG4000, tris(hydroxymethyl)aminomethane, isopropanol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.2K	Resolution 2.10 Å R-free 0.253
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 595–660	Fragment：N-TERMINAL DOMAIN	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；277.2 K；PEG4000, tris(hydroxymethyl)aminomethane, isopropanol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.2K	Resolution 2.10 Å R-free 0.253
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 595–660	Fragment：N-TERMINAL DOMAIN	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；277.2 K；PEG4000, tris(hydroxymethyl)aminomethane, isopropanol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.2K	Resolution 2.10 Å R-free 0.253

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 1GCP	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1F5X NMR STRUCTURE OF THE Y174 AUTOINHIBITED DBL HOMOLOGY DOMAIN Deposited 2000-06-18	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 168–375（208 aa） Fragment：DBL HOMOLOGY DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 70 mM；Pressure ambient NMR sample composition 1.4 mM 15N,13C,2H; 20 mM phosphate buffer; 50 mM NaCl; 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
1GCQ CRYSTAL STRUCTURE OF VAV AND GRB2 SH3 DOMAINS Deposited 2000-08-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 595–660（66 aa） Fragment：N-TERMINAL SH3 DOMAIN	Not recorded	MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293.2 K；2-methyl-2,4-pentanediol, imidazole, magnesium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.2K	Resolution 1.68 Å R-free 0.235
1K1Z Solution structure of N-terminal SH3 domain mutant(P33G) of murine Vav Deposited 2001-09-26	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 583–660（78 aa） Fragment：N-terminal SH3 domain	Mutation：P33G	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；298 K；Pressure 1 NMR sample composition 1.5mM protein U-15N,13C; 10mM phosphate buffer K; 10mM DTT-d \| 90% H2O/10% D2O	Resolution not provided
2KBT Attachment of an NMR-invisible solubility enhancement tag (INSET) using a sortase-mediated protein ligation method Deposited 2008-12-07	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 784–844（61 aa） Fragment：SH3 2 domain of Proto-oncogene vav,UNP residues 228-282 of Immunoglobulin G-binding protein G	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 150；Pressure ambient NMR sample composition 20 mM MES-1, 2 mM DTT-2, 150 mM NaCl-3, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2VRW Critical structural role for the PH and C1 domains of the Vav1 exchange factor Deposited 2008-04-16	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 B 170–575（406 aa） Fragment：RESIDUES 170-575	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 9；100MM BICINE PH9.0 10% PEG 6000	Resolution 1.85 Å R-free 0.251

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

View Construct and Data Evidence

UniProt name	VAV_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–70； UniProt 595–660 Author chain B； PDBConstruct 5–70； UniProt 595–660 Author chain C； PDBConstruct 5–70； UniProt 595–660 Author chain D； PDBConstruct 5–70； UniProt 595–660

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	1gcp
Deposition date deposition_date	2000-08-08
Structure title title	CRYSTAL STRUCTURE OF VAV SH3 DOMAIN
Keywords keywords	SH3 DOMAIN, VAV, 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	21.37 Å
Radius of gyration Rg (electron density) rg_electron	20.68 Å
Forward intensity I(0) i0	15858900.00
Molecular weight molecular_weight	30262.0 kDa
Excluded volume excluded_volume	37812 Å³
Envelope volume envelope_volume	44941 Å³
Hydration-shell volume shell_volume	19090 Å³
Envelope diameter envelope_diameter	73.9 Å
Shell Rg shell_rg	26.27 Å
Envelope Rg envelope_rg	20.75 Å
Shape Rg shape_rg	20.68 Å
Total Rg total_rg	21.48 Å
Total atoms total_atoms	2151
Residues n_residues	262
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	74.3 Å
Rg (real space) rg_real	21.41 Å
Rg uncertainty (real space) rg_real_error	0.70 Å
I(0) (real space) i0_real	1.5860e+07
I(0) uncertainty (real space) i0_real_error	2.2260e+05
Rg (reciprocal space) rg_reciprocal	21.41 Å
I(0) (reciprocal space) i0_reciprocal	15860000.0000
Solution quality estimate total_estimate	0.8635
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.1 Å
Skewness Skewness skewness	0.418
Kurtosis Kurtosis kurtosis	-0.178
Angular range angular_range	— – 0.3700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6268000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.781; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.908; Smooth: 0.971

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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) 9 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d1gcpa_
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.2 — SH3-domain
Family Family family	b.34.2.1 — SH3-domain

Domain ID domain_id	d1gcpb1
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.2 — SH3-domain
Family Family family	b.34.2.1 — SH3-domain

Domain ID domain_id	d1gcpb2
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	d1gcpc_
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.2 — SH3-domain
Family Family family	b.34.2.1 — SH3-domain

Domain ID domain_id	d1gcpd_
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.2 — SH3-domain
Family Family family	b.34.2.1 — SH3-domain

CATH v4.4 (4 domains)

Domain ID domain_id	1gcpA00
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	1gcpB00
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	1gcpC00
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	1gcpD00
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	32.205 Å
Unit-cell length b length_b	101.115 Å
Unit-cell length c length_c	39.707 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.34 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.1960
R_work r_work	0.1930
R_free r_free	0.2530

Description description	VAV PROTO-ONCOGENE
Molecular weight formula_weight	8030.0 kDa
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	2341

CRYSTAL STRUCTURE OF VAV SH3 DOMAIN

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

VAV PROTO-ONCOGENE

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) 9 domains

SCOP 2.08 (5 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI Class编号 ncbi_taxonomy_id	10090
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	190

fit	/app/data/saxs_computation/gc/1gcp/1gcp.fit
pddf	/app/data/pr_computation/gc/1gcp/1gcp.pr.out
profile	/app/data/saxs_computation/gc/1gcp/1gcp.dat