SAXSdb — 3rab

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

PROTEIN (RAB3A)

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 18–186	Fragment：GTPASE DOMAIN	MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；CRYSTALLIZATION CONDITIONS: 14%PEG-8000,50 MM NAMES, PH 6.5, 200 MM NACL	Resolution 2.00 Å R-free 0.237

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 3RAB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1ZBD STRUCTURAL BASIS OF RAB EFFECTOR SPECIFICITY: CRYSTAL STRUCTURE OF THE SMALL G PROTEIN RAB3A COMPLEXED WITH THE EFFECTOR DOMAIN OF RABPHILIN-3A Deposited 1998-11-06	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 19–217（199 aa） Fragment：19-217	Mutation：Q81L Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；pH 8.0	Resolution 2.60 Å R-free 0.263
1ZBD STRUCTURAL BASIS OF RAB EFFECTOR SPECIFICITY: CRYSTAL STRUCTURE OF THE SMALL G PROTEIN RAB3A COMPLEXED WITH THE EFFECTOR DOMAIN OF RABPHILIN-3A Deposited 1998-11-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 19–217（199 aa） Fragment：19-217	Mutation：Q81L Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；pH 8.0	Resolution 2.60 Å R-free 0.263

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

View Construct and Data Evidence

UniProt name	RAB3A_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–169； UniProt 18–186

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	3rab
Deposition date deposition_date	1998-11-16
Structure title title	GPPNHP-BOUND RAB3A AT 2.0 A RESOLUTION
Keywords keywords	G PROTEIN, VESICULAR TRAFFICKING, GTP HYDROLYSIS, RAB PROTEIN, NEUROTRANSMITTER RELEASE, HYDROLASE; HYDROLASE
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	16.44 Å
Radius of gyration Rg (electron density) rg_electron	15.19 Å
Forward intensity I(0) i0	7570510.00
Molecular weight molecular_weight	19850.0 kDa
Excluded volume excluded_volume	24676 Å³
Envelope volume envelope_volume	26895 Å³
Hydration-shell volume shell_volume	14772 Å³
Envelope diameter envelope_diameter	50.9 Å
Shell Rg shell_rg	21.33 Å
Envelope Rg envelope_rg	15.56 Å
Shape Rg shape_rg	15.19 Å
Total Rg total_rg	16.25 Å
Total atoms total_atoms	1397
Residues n_residues	169
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	52.4 Å
Rg (real space) rg_real	16.32 Å
Rg uncertainty (real space) rg_real_error	0.28 Å
I(0) (real space) i0_real	7.5710e+06
I(0) uncertainty (real space) i0_real_error	7.9960e+04
Rg (reciprocal space) rg_reciprocal	16.34 Å
I(0) (reciprocal space) i0_reciprocal	7571000.0000
Solution quality estimate total_estimate	0.8887
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.5 Å
Skewness Skewness skewness	0.126
Kurtosis Kurtosis kurtosis	-0.374
Angular range angular_range	— – 0.4850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1258000.0000
Real-space data points n_real_points	79
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.864; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.966

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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	PROTEIN (RAB3A)
Molecular weight formula_weight	19655.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1520

NFDYMFKILIIGNSSVGKTSFLFRYADDSFTPAFVSTVGIDFKVKTIYRNDKRIKLQIWDTAGQERYRTITTAYYRGAMGFILMYDITNEESFNAVQDWSTQIKTYSWDNAQVLLVGNKCDMEDERVVSSERGRQLADHLGFEFFEASAKDNINVKQTFERLVDVICEK

来源 Source

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 BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
Molecular weight formula_weight	522.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	123

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3raba_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.8 — G proteins

CATH v4.4 (1 domains)

Domain ID domain_id	3rabA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

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8. Citations (1)

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Unit-cell length a length_a	88.900 Å
Unit-cell length b length_b	35.000 Å
Unit-cell length c length_c	58.600 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	107.20 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	—
R_work r_work	0.1910
R_free r_free	0.2370

fit	/app/data/saxs_computation/ra/3rab/3rab.fit
pddf	/app/data/pr_computation/ra/3rab/3rab.pr.out
profile	/app/data/saxs_computation/ra/3rab/3rab.dat

GPPNHP-BOUND RAB3A AT 2.0 A RESOLUTION

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

PROTEIN (RAB3A)

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