SAXSdb — 9mf1

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

GTP-binding protein Rit1

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 2–197	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 9；293 K；10% w/v PEG 6000, 0.1M Bicine pH 9.0	Resolution 2.20 Å R-free 0.230

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 9MF1	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4KLZ Inhibition of Small GTPases by Stabilization of the GDP Complex, a Novel Approach applied to Rit1, a Target for Rheumatoid Arthritis Deposited 2013-05-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 19–189（171 aa） Fragment：GTP binding domain, unp residues 19-189	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；11-14% w/v PEG4000, 5-8% v/v Jeffamine M600, imidazole , VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 2.30 Å R-free 0.311
9MEY Crystal structure of RIT1(GDP) bound to LZTR1(Kelch domain) Deposited 2024-12-09	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 2–197（196 aa）	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.2；277 K；44% Morpheus II PPT7, 100mM MonoSach II, 100mM MB6 buffer pH 8.2	Resolution 2.95 Å R-free 0.256
9MEY Crystal structure of RIT1(GDP) bound to LZTR1(Kelch domain) Deposited 2024-12-09	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 2–197（196 aa）	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.2；277 K；44% Morpheus II PPT7, 100mM MonoSach II, 100mM MB6 buffer pH 8.2	Resolution 2.95 Å R-free 0.256

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

View Construct and Data Evidence

UniProt name	RIT1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–197； UniProt 2–197

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	9mf1
Deposition date deposition_date	2024-12-09
Structure title title	Crystal structure of RIT1 in the GDP state
Keywords keywords	Substrate adaptor, ONCOPROTEIN; ONCOPROTEIN
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	17.41 Å
Radius of gyration Rg (electron density) rg_electron	16.11 Å
Forward intensity I(0) i0	9144770.00
Molecular weight molecular_weight	21453.0 kDa
Excluded volume excluded_volume	26568 Å³
Envelope volume envelope_volume	30868 Å³
Hydration-shell volume shell_volume	15968 Å³
Envelope diameter envelope_diameter	62.4 Å
Shell Rg shell_rg	22.40 Å
Envelope Rg envelope_rg	16.63 Å
Shape Rg shape_rg	16.11 Å
Total Rg total_rg	17.19 Å
Total atoms total_atoms	1503
Residues n_residues	178
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	62.2 Å
Rg (real space) rg_real	17.31 Å
Rg uncertainty (real space) rg_real_error	0.42 Å
I(0) (real space) i0_real	9.1450e+06
I(0) uncertainty (real space) i0_real_error	1.1420e+05
Rg (reciprocal space) rg_reciprocal	17.33 Å
I(0) (reciprocal space) i0_reciprocal	9145000.0000
Solution quality estimate total_estimate	0.7601
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.4 Å
Skewness Skewness skewness	0.212
Kurtosis Kurtosis kurtosis	-0.160
Angular range angular_range	— – 0.4550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2015000.0000
Real-space data points n_real_points	76
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.631; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	GTP-binding protein Rit1
Molecular weight formula_weight	22464.6 kDa
EC 编号 ec_number	3.6.5.2
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	1667

GDSGTRPVGSCCSSPAGLSREYKLVMLGAGGVGKSAMTMQFISHRFPEDHDPTIEDAYKIRIRIDDEPANLDILDTAGQAEFTAMRDQYMRAGEGFIICYSITDRRSFHEVREFKQLIYRVRRTDDTPVVLVGNKSDLKQLRQVTKEEGLALAREFSCPFFETSAAYRYYIDDVFHALVREIRRKEKEAVLAMEKKS

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

Entity 2 Entity 2 non-polymer

Description description	GUANOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	443.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

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

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	nat
Copy count entity_count	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	158

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8. Citations (1)

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Unit-cell length a length_a	35.577 Å
Unit-cell length b length_b	66.155 Å
Unit-cell length c length_c	124.717 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	4

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

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	45.380 Å
R factor r_factor	0.1822
R_work r_work	0.1797
R_free r_free	0.2304

fit	/app/data/saxs_computation/mf/9mf1/9mf1.fit
pddf	/app/data/pr_computation/mf/9mf1/9mf1.pr.out
profile	/app/data/saxs_computation/mf/9mf1/9mf1.dat

Crystal structure of RIT1 in the GDP state

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

GTP-binding protein Rit1

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