SAXSdb — 1srq

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

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 75–415 Chain B； UniProt 75–415	Fragment：Residues 75-415, catalytic fragment Mutation：Q204A	SO4 SULFATE ION × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.1；277 K；PEG 3350, MPD, magnesium sulfate, HEPES, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.90 Å R-free 0.276
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 75–415 Chain D； UniProt 75–415	Fragment：Residues 75-415, catalytic fragment Mutation：Q204A	SO4 SULFATE ION × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.1；277 K；PEG 3350, MPD, magnesium sulfate, HEPES, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.90 Å R-free 0.276

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 1SRQ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3BRW Structure of the Rap-RapGAP complex Deposited 2007-12-21	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 75–415（341 aa） Fragment：Rap1GAP, UNP residues 75-415	Mutation：Q204A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；285 K；8-11% PEG 2000 MME, 100mM MES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K	Resolution 3.40 Å R-free 0.280
3BRW Structure of the Rap-RapGAP complex Deposited 2007-12-21	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 75–415（341 aa） Fragment：Rap1GAP, UNP residues 75-415	Mutation：Q204A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；285 K；8-11% PEG 2000 MME, 100mM MES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K	Resolution 3.40 Å R-free 0.280
3BRW Structure of the Rap-RapGAP complex Deposited 2007-12-21	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 75–415（341 aa） Fragment：Rap1GAP, UNP residues 75-415	Mutation：Q204A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；285 K；8-11% PEG 2000 MME, 100mM MES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K	Resolution 3.40 Å R-free 0.280

1 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RGP2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–341； UniProt 75–415 Author chain B； PDBConstruct 1–341； UniProt 75–415 Author chain C； PDBConstruct 1–341； UniProt 75–415 Author chain D； PDBConstruct 1–341； UniProt 75–415

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	1srq
Deposition date deposition_date	2004-03-23
Structure title title	Crystal Structure of the Rap1GAP catalytic domain
Keywords keywords	MIXED ALPHA-BETA, 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	42.12 Å
Radius of gyration Rg (electron density) rg_electron	42.07 Å
Forward intensity I(0) i0	190720000.00
Molecular weight molecular_weight	115920.0 kDa
Excluded volume excluded_volume	146430 Å³
Envelope volume envelope_volume	210050 Å³
Hydration-shell volume shell_volume	44574 Å³
Envelope diameter envelope_diameter	138.4 Å
Shell Rg shell_rg	44.23 Å
Envelope Rg envelope_rg	40.91 Å
Shape Rg shape_rg	42.08 Å
Total Rg total_rg	42.18 Å
Total atoms total_atoms	8194
Residues n_residues	1024
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	141.2 Å
Rg (real space) rg_real	42.24 Å
Rg uncertainty (real space) rg_real_error	1.36 Å
I(0) (real space) i0_real	1.9070e+08
I(0) uncertainty (real space) i0_real_error	3.8140e+06
Rg (reciprocal space) rg_reciprocal	42.12 Å
I(0) (reciprocal space) i0_reciprocal	190700000.0000
Solution quality estimate total_estimate	0.8790
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	53.4 Å
Skewness Skewness skewness	0.293
Kurtosis Kurtosis kurtosis	-0.646
Angular range angular_range	— – 0.1850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	14840000.0000
Real-space data points n_real_points	38
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.871; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.905; Smooth: 0.904

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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	GTPase-activating protein 1
Molecular weight formula_weight	38958.3 kDa
Mutation mutation	Q204A
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	8241

PTTKVKLECNPTARIYRKHFLGKEHFNYYSLDTALGHLVFSLKYDVIGDQEHLRLLLRTKCRTYHDVIPISCLTEFPNVVQMAKLVCEDVNVDRFYPVLYPKASRLIVTFDEHVISNNFKFGVIYQKLGQTSEEELFSTNEESPAFVEFLEFLGQKVKLQDFKGFRGGLDVTHGQTGTESVYCNFRNKEIMFHVSTKLPYTEGDAQQLQRKRHIGNDIVAVVFQDENTPFVPDMIASNFLHAYVVVQAEGGGPDGPLYKVSVTARDDVPFFGPPLPDPAVFRKGPEFQEFLLTKLINAEYACYKAEKFAKLEERTRAALLETLYEELHIHSQSMMGLGGDE

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 BL21(DE3)

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 non-polymer

Description description	(4S)-2-METHYL-2,4-PENTANEDIOL
Molecular weight formula_weight	118.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	47

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7. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1srqa_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.55 — Rap/Ran-GAP
Superfamily Superfamily superfamily	e.55.1 — Rap/Ran-GAP
Family Family family	e.55.1.1 — Rap/Ran-GAP

Domain ID domain_id	d1srqb_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.55 — Rap/Ran-GAP
Superfamily Superfamily superfamily	e.55.1 — Rap/Ran-GAP
Family Family family	e.55.1.1 — Rap/Ran-GAP

Domain ID domain_id	d1srqc_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.55 — Rap/Ran-GAP
Superfamily Superfamily superfamily	e.55.1 — Rap/Ran-GAP
Family Family family	e.55.1.1 — Rap/Ran-GAP

Domain ID domain_id	d1srqd_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.55 — Rap/Ran-GAP
Superfamily Superfamily superfamily	e.55.1 — Rap/Ran-GAP
Family Family family	e.55.1.1 — Rap/Ran-GAP

CATH v4.4 (7 domains)

Domain ID domain_id	1srqA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1120 — Arylsulfatase, C-terminal domain
Homologous superfamily homologous superfamily	160 —

Domain ID domain_id	1srqA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	11210 — Rap/Ran-GAP

Domain ID domain_id	1srqB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1120 — Arylsulfatase, C-terminal domain
Homologous superfamily homologous superfamily	160 —

Domain ID domain_id	1srqB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	11210 — Rap/Ran-GAP

Domain ID domain_id	1srqC01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1120 — Arylsulfatase, C-terminal domain
Homologous superfamily homologous superfamily	160 —

Domain ID domain_id	1srqC02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	11210 — Rap/Ran-GAP

Domain ID domain_id	1srqD01
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	210 —

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8. Citations (1)

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Unit-cell length a length_a	170.700 Å
Unit-cell length b length_b	224.500 Å
Unit-cell length c length_c	48.700 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	14.990 Å
R factor r_factor	0.2340
R_work r_work	0.2318
R_free r_free	0.2760

fit	/app/data/saxs_computation/sr/1srq/1srq.fit
pddf	/app/data/pr_computation/sr/1srq/1srq.pr.out
profile	/app/data/saxs_computation/sr/1srq/1srq.dat

Crystal Structure of the Rap1GAP catalytic domain

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

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