SAXSdb — 3wps

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

Rac GTPase-activating protein 1

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 346–546 Chain B； UniProt 346–546	Fragment：UNP residues 346-546 Mutation：S387D Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；2.0M magnesium sulfate, 0.1M MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.70 Å R-free 0.259

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 3WPS	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2OVJ The crystal structure of the human Rac GTPase activating protein 1 (RACGAP1) MgcRacGAP. Deposited 2007-02-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 348–546（199 aa） Fragment：Rho-GAP domain	Not recorded	7PE 2-(2-(2-(2-(2-(2-ETHOXYETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHANOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；298 K；25% PEG 3350, 0.1M BIS-TRIS, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.49 Å R-free 0.176
3W6R Crystal structure of the GAP domain of human MgcRacGAP Deposited 2013-02-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 348–546（199 aa） Fragment：Rho-GAP domain, UNP RESIDUES 348-546	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.7；295 K；100mM sodium cacodylate buffer, 13% polyethylene glycol 6000, 25% glycerol, pH 5.7, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 1.90 Å R-free 0.259
3WPQ crystal structure of the GAP domain of MgcRacGAP(S387A) Deposited 2014-01-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 346–546（201 aa） Fragment：UNP residues 346-546	Mutation：S387A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；1.0M Na Citrate, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.84 Å R-free 0.200
3WPQ crystal structure of the GAP domain of MgcRacGAP(S387A) Deposited 2014-01-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 346–546（201 aa） Fragment：UNP residues 346-546	Mutation：S387A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；1.0M Na Citrate, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.84 Å R-free 0.200
4B6D Structure of the atypical C1 domain of MgcRacGAP Deposited 2012-08-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 284–339（56 aa） Fragment：C1 DOMAIN, RESIDUES 284-339	Not recorded	GOL GLYCEROL × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.1；1.3 M SODIUM CITRATE, PH 7.1 AND 0.3 M DIMETHYLETHYLAMMONIUM PROPANE SULFONATE	Resolution 2.20 Å R-free 0.235
4B6D Structure of the atypical C1 domain of MgcRacGAP Deposited 2012-08-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 284–339（56 aa） Fragment：C1 DOMAIN, RESIDUES 284-339	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.1；1.3 M SODIUM CITRATE, PH 7.1 AND 0.3 M DIMETHYLETHYLAMMONIUM PROPANE SULFONATE	Resolution 2.20 Å R-free 0.235
4B6D Structure of the atypical C1 domain of MgcRacGAP Deposited 2012-08-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 284–339（56 aa） Fragment：C1 DOMAIN, RESIDUES 284-339	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.1；1.3 M SODIUM CITRATE, PH 7.1 AND 0.3 M DIMETHYLETHYLAMMONIUM PROPANE SULFONATE	Resolution 2.20 Å R-free 0.235
4B6D Structure of the atypical C1 domain of MgcRacGAP Deposited 2012-08-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 284–339（56 aa） Fragment：C1 DOMAIN, RESIDUES 284-339	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.1；1.3 M SODIUM CITRATE, PH 7.1 AND 0.3 M DIMETHYLETHYLAMMONIUM PROPANE SULFONATE	Resolution 2.20 Å R-free 0.235
4B6D Structure of the atypical C1 domain of MgcRacGAP Deposited 2012-08-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 284–339（56 aa） Fragment：C1 DOMAIN, RESIDUES 284-339	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.1；1.3 M SODIUM CITRATE, PH 7.1 AND 0.3 M DIMETHYLETHYLAMMONIUM PROPANE SULFONATE	Resolution 2.20 Å R-free 0.235
4B6D Structure of the atypical C1 domain of MgcRacGAP Deposited 2012-08-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain F 284–339（56 aa） Fragment：C1 DOMAIN, RESIDUES 284-339	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.1；1.3 M SODIUM CITRATE, PH 7.1 AND 0.3 M DIMETHYLETHYLAMMONIUM PROPANE SULFONATE	Resolution 2.20 Å R-free 0.235
5C2J Complex structure of the GAP domain of MgcRacGAP and Cdc42 Deposited 2015-06-16	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 346–546（201 aa） Fragment：GAP domain, UNP residues 346-546	Not recorded	MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 AF3 ALUMINUM FLUORIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；PEG3350, Bis-Tris	Resolution 2.50 Å R-free 0.263
5C2K Crystal structure of the fusion protein linked by RhoA and the GAP domain of MgcRacGAP Deposited 2015-06-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 346–546（201 aa） Fragment：GAP domain, UNP residues 346-546	Mutation：S249D	MG MAGNESIUM ION × 1 AF3 ALUMINUM FLUORIDE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；PEG3350, Bis-Tris	Resolution 1.42 Å R-free 0.206

6 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RGAP1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 8–208； UniProt 346–546 Author chain B； PDBConstruct 8–208； UniProt 346–546

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	3wps
Deposition date deposition_date	2014-01-15
Structure title title	crystal structure of the GAP domain of MgcRacGAP(S387D)
Keywords keywords	GTPase activation, small G-proteins, 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	25.46 Å
Radius of gyration Rg (electron density) rg_electron	24.80 Å
Forward intensity I(0) i0	37215700.00
Molecular weight molecular_weight	46396.0 kDa
Excluded volume excluded_volume	57585 Å³
Envelope volume envelope_volume	69286 Å³
Hydration-shell volume shell_volume	23943 Å³
Envelope diameter envelope_diameter	88.4 Å
Shell Rg shell_rg	31.21 Å
Envelope Rg envelope_rg	25.20 Å
Shape Rg shape_rg	24.82 Å
Total Rg total_rg	25.49 Å
Total atoms total_atoms	3186
Residues n_residues	384
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	86.3 Å
Rg (real space) rg_real	25.54 Å
Rg uncertainty (real space) rg_real_error	0.81 Å
I(0) (real space) i0_real	3.7220e+07
I(0) uncertainty (real space) i0_real_error	6.2040e+05
Rg (reciprocal space) rg_reciprocal	25.52 Å
I(0) (reciprocal space) i0_reciprocal	37220000.0000
Solution quality estimate total_estimate	0.7844
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.8 Å
Skewness Skewness skewness	0.443
Kurtosis Kurtosis kurtosis	-0.354
Angular range angular_range	— – 0.3100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4436000.0000
Real-space data points n_real_points	63
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.750; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.953; 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	Rac GTPase-activating protein 1
Molecular weight formula_weight	23643.0 kDa
Mutation mutation	S387D
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	3279

GSSGSSGIGEGMLADFVSQTSPMIPSIVVHCVNEIEQRGLTETGLYRIDGCDRTVKELKEKFLRVKTVPLLSKVDDIHAICSLLKDFLRNLKEPLLTFRLNRAFMEAAEITDEDNSIAAMYQAVGELPQANRDTLAFLMIHLQRVAQSPHTKMDVANLAKVFGPTIVAHAVPNPDPVTMSQDIKRQPKVVERLLSLPLEYWSQFMMVE

来源 Source

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 KRX

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	93

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3wpsa_
Class class	a — All alpha proteins
Fold Fold fold	a.116 — GTPase activation domain, GAP
Superfamily Superfamily superfamily	a.116.1 — GTPase activation domain, GAP
Family Family family	a.116.1.0 — automated matches

Domain ID domain_id	d3wpsb_
Class class	a — All alpha proteins
Fold Fold fold	a.116 — GTPase activation domain, GAP
Superfamily Superfamily superfamily	a.116.1 — GTPase activation domain, GAP
Family Family family	a.116.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	3wpsA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	555 — Phosphatidylinositol 3-kinase; Chain A
Homologous superfamily homologous superfamily	10 — Rho GTPase activation protein

Domain ID domain_id	3wpsB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	555 — Phosphatidylinositol 3-kinase; Chain A
Homologous superfamily homologous superfamily	10 — Rho GTPase activation protein

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8. Citations (1)

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Unit-cell length a length_a	77.321 Å
Unit-cell length b length_b	77.321 Å
Unit-cell length c length_c	108.744 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	6

Space group space_group	P 31
Space-group number int_tables_number	144
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	38.660 Å
R factor r_factor	0.2100
R_work r_work	0.2100
R_free r_free	0.2590

fit	/app/data/saxs_computation/wp/3wps/3wps.fit
pddf	/app/data/pr_computation/wp/3wps/3wps.pr.out
profile	/app/data/saxs_computation/wp/3wps/3wps.dat

crystal structure of the GAP domain of MgcRacGAP(S387D)

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

Rac GTPase-activating protein 1

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