SAXSdb — 2cls

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

RHO-RELATED GTP-BINDING PROTEIN RHO6

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 5–200	Fragment：RESIDUES 5-200	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8.5；0.2M NAI, 20%(W/V)PEG3350, 0.1M BISTRISPROPANE PH8.5, 10% (V/V) ETHYLENE GLYCOL, 0.5% (V/V) DIMETHYLSULPHOXIDE, pH 8.50	Resolution 2.31 Å R-free 0.236
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 5–200	Fragment：RESIDUES 5-200	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8.5；0.2M NAI, 20%(W/V)PEG3350, 0.1M BISTRISPROPANE PH8.5, 10% (V/V) ETHYLENE GLYCOL, 0.5% (V/V) DIMETHYLSULPHOXIDE, pH 8.50	Resolution 2.31 Å R-free 0.236

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 2CLS	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2REX Crystal structure of the effector domain of PLXNB1 bound with Rnd1 GTPase Deposited 2007-09-27	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 B 5–200（196 aa） Fragment：Residues 5-200	Not recorded	UNX UNKNOWN LIGAND × 15 MG MAGNESIUM ION × 1 CA CALCIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；20% PEG 3350, 0.2M Calcium chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.30 Å R-free 0.248
2REX Crystal structure of the effector domain of PLXNB1 bound with Rnd1 GTPase Deposited 2007-09-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 5–200（196 aa） Fragment：Residues 5-200	Not recorded	UNX UNKNOWN LIGAND × 15 MG MAGNESIUM ION × 1 CA CALCIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；20% PEG 3350, 0.2M Calcium chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.30 Å R-free 0.248
2REX Crystal structure of the effector domain of PLXNB1 bound with Rnd1 GTPase Deposited 2007-09-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 5–200（196 aa） Fragment：Residues 5-200 Chain D 5–200（196 aa） Fragment：Residues 5-200	Not recorded	UNX UNKNOWN LIGAND × 30 MG MAGNESIUM ION × 2 CA CALCIUM ION × 2 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；20% PEG 3350, 0.2M Calcium chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.30 Å R-free 0.248
2REX Crystal structure of the effector domain of PLXNB1 bound with Rnd1 GTPase Deposited 2007-09-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain B 5–200（196 aa） Fragment：Residues 5-200 Chain D 5–200（196 aa） Fragment：Residues 5-200	Not recorded	UNX UNKNOWN LIGAND × 60 MG MAGNESIUM ION × 4 CA CALCIUM ION × 4 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；20% PEG 3350, 0.2M Calcium chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.30 Å R-free 0.248
2REX Crystal structure of the effector domain of PLXNB1 bound with Rnd1 GTPase Deposited 2007-09-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 5–200（196 aa） Fragment：Residues 5-200 Chain D 5–200（196 aa） Fragment：Residues 5-200	Not recorded	UNX UNKNOWN LIGAND × 30 MG MAGNESIUM ION × 2 CA CALCIUM ION × 2 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；20% PEG 3350, 0.2M Calcium chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.30 Å R-free 0.248
3Q3J Crystal structure of plexin A2 RBD in complex with Rnd1 Deposited 2010-12-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain B 5–200（196 aa） Fragment：UNP residues 5-200	Not recorded	UNX UNKNOWN LIGAND × 36 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 4 MG MAGNESIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions vapor diffusion, sitting drops；pH 7.5；293 K；The complex sample (2.7 mg/mL) was incubated with 5mM Gpp(NH)p. Crystallization cocktail: 25.5% PEG3350, 0.2 M magnesium chloride, 0.1M Hepes. Seeding was applied in the production of the diffraction-quality crystal., pH 7.5, vapor diffusion, sitting drops, temperature 293K	Resolution 1.97 Å R-free 0.248

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

View Construct and Data Evidence

UniProt name	RND1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–198； UniProt 5–200 Author chain B； PDBConstruct 3–198； UniProt 5–200

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	2cls
Deposition date deposition_date	2006-04-28
Structure title title	The crystal structure of the human RND1 GTPase in the active GTP bound state
Keywords keywords	;NUCLEOTIDE-BINDING, GTP-BINDING PROTEIN RHO6, MEMBRANE, PRENYLATION, LIPOPROTEIN, GTP-BINDING, CYTOSKELETON, SMALL GTPASE, NUCLEOTIDE BINDING PROTEIN ;; NUCLEOTIDE BINDING 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	24.77 Å
Radius of gyration Rg (electron density) rg_electron	24.26 Å
Forward intensity I(0) i0	28009700.00
Molecular weight molecular_weight	39799.0 kDa
Excluded volume excluded_volume	49373 Å³
Envelope volume envelope_volume	60023 Å³
Hydration-shell volume shell_volume	21441 Å³
Envelope diameter envelope_diameter	81.6 Å
Shell Rg shell_rg	30.38 Å
Envelope Rg envelope_rg	24.48 Å
Shape Rg shape_rg	24.25 Å
Total Rg total_rg	25.00 Å
Total atoms total_atoms	2774
Residues n_residues	357
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	82.0 Å
Rg (real space) rg_real	24.87 Å
Rg uncertainty (real space) rg_real_error	0.71 Å
I(0) (real space) i0_real	2.8010e+07
I(0) uncertainty (real space) i0_real_error	3.9450e+05
Rg (reciprocal space) rg_reciprocal	24.85 Å
I(0) (reciprocal space) i0_reciprocal	28010000.0000
Solution quality estimate total_estimate	0.7781
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	22.1 Å
Skewness Skewness skewness	0.353
Kurtosis Kurtosis kurtosis	-0.667
Angular range angular_range	— – 0.3200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5275000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.778; Stabil: 0.983; Sysdev: 1.000; Positv: 1.000; Valcen: 0.831; Smooth: 0.000

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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	RHO-RELATED GTP-BINDING PROTEIN RHO6
Molecular weight formula_weight	22107.4 kDa
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	2918

SMRAPQPVVARCKLVLVGDVQCGKTAMLQVLAKDCYPETYVPTVFENYTACLETEEQRVELSLWDTSGSPYYDNVRPLCYSDSDAVLLCFDISRPETVDSALKKWRTEILDYCPSTRVLLIGCKTDLRTDLSTLMELSHQKQAPISYEQGCAIAKQLGAEIYLEGSAFTSEKSIHSIFRTASMLCLNKPSPLPQKSPV

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	GUANOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	523.2 kDa
Source method src_method	syn
Copy count entity_count	2

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	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	129

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2clsa_
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

Domain ID domain_id	d2clsb_
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 (2 domains)

Domain ID domain_id	2clsA00
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

Domain ID domain_id	2clsB00
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	67.168 Å
Unit-cell length b length_b	67.762 Å
Unit-cell length c length_c	206.409 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.310 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2070
R_work r_work	0.2050
R_free r_free	0.2360

fit	/app/data/saxs_computation/cl/2cls/2cls.fit
pddf	/app/data/pr_computation/cl/2cls/2cls.pr.out
profile	/app/data/saxs_computation/cl/2cls/2cls.dat

The crystal structure of the human RND1 GTPase in the active GTP bound state

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

RHO-RELATED GTP-BINDING PROTEIN RHO6

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