SAXSdb — 4b6d

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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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 284–339	Fragment：C1 DOMAIN, RESIDUES 284-339	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
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 284–339	Fragment：C1 DOMAIN, RESIDUES 284-339	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
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 284–339	Fragment：C1 DOMAIN, RESIDUES 284-339	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
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 284–339	Fragment：C1 DOMAIN, RESIDUES 284-339	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
5	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain E； UniProt 284–339	Fragment：C1 DOMAIN, RESIDUES 284-339	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
6	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain F； UniProt 284–339	Fragment：C1 DOMAIN, RESIDUES 284-339	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

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 4B6D	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 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 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 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 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
3WPS crystal structure of the GAP domain of MgcRacGAP(S387D) 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 homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 346–546（201 aa） Fragment：UNP residues 346-546 Chain B 346–546（201 aa） Fragment：UNP residues 346-546	Mutation：S387D Non-standard monomer：Yes (specific site not provided by mmCIF) 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
5C2J Complex structure of the GAP domain of MgcRacGAP and Cdc42 Deposited 2015-06-16	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 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 7 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 6–61； UniProt 284–339 Author chain B； PDBConstruct 6–61； UniProt 284–339 Author chain C； PDBConstruct 6–61； UniProt 284–339 Author chain D； PDBConstruct 6–61； UniProt 284–339 Author chain E； PDBConstruct 6–61； UniProt 284–339 Author chain F； PDBConstruct 6–61； UniProt 284–339

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	4b6d
Deposition date deposition_date	2012-08-09
Structure title title	Structure of the atypical C1 domain of MgcRacGAP
Keywords keywords	SIGNALING PROTEIN, CYTOKINESIS, PLASMA MEMBRANE, PHOSPHOLIPIDS, CENTRALSPINDLIN, SPINDLE MIDZONE, CENTRAL SPINDLE, MIDBODY; 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	23.65 Å
Radius of gyration Rg (electron density) rg_electron	23.62 Å
Forward intensity I(0) i0	30885300.00
Molecular weight molecular_weight	40459.0 kDa
Excluded volume excluded_volume	49924 Å³
Envelope volume envelope_volume	64862 Å³
Hydration-shell volume shell_volume	23645 Å³
Envelope diameter envelope_diameter	87.2 Å
Shell Rg shell_rg	29.74 Å
Envelope Rg envelope_rg	23.77 Å
Shape Rg shape_rg	23.69 Å
Total Rg total_rg	24.15 Å
Total atoms total_atoms	2752
Residues n_residues	354
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	84.5 Å
Rg (real space) rg_real	23.70 Å
Rg uncertainty (real space) rg_real_error	0.78 Å
I(0) (real space) i0_real	3.0890e+07
I(0) uncertainty (real space) i0_real_error	4.8150e+05
Rg (reciprocal space) rg_reciprocal	23.69 Å
I(0) (reciprocal space) i0_reciprocal	30890000.0000
Solution quality estimate total_estimate	0.8504
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.4 Å
Skewness Skewness skewness	0.421
Kurtosis Kurtosis kurtosis	-0.198
Angular range angular_range	— – 0.3350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3567000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.722; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.894; Smooth: 0.993

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	RAC GTPASE-ACTIVATING PROTEIN 1
Molecular weight formula_weight	6823.3 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	2932

GPLGSMRLHDFVSKTVIKPESCVPCGKRIKFGKLSLKCRDCRVVSHPECRDRCPLPCIPTL

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

Entity 2 Entity 2 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	163

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7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	4b6dA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	4b6dB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	4b6dC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	4b6dD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	4b6dE00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	4b6dF00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily	20 —

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8. Citations (1)

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Unit-cell length a length_a	36.850 Å
Unit-cell length b length_b	133.850 Å
Unit-cell length c length_c	56.682 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	109.03 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

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

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	66.925 Å
R factor r_factor	0.2125
R_work r_work	0.2103
R_free r_free	0.2355

fit	/app/data/saxs_computation/b6/4b6d/4b6d.fit
pddf	/app/data/pr_computation/b6/4b6d/4b6d.pr.out
profile	/app/data/saxs_computation/b6/4b6d/4b6d.dat

Structure of the atypical C1 domain of MgcRacGAP

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