SAXSdb — 1byu

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

PROTEIN (GTP-BINDING PROTEIN RAN)

Canis lupus familiaris

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 1–216 Chain B； UniProt 1–216	Fragment：ALL	MG MAGNESIUM ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.2；SEE PUBLICATION, pH 7.2	Resolution 2.15 Å R-free 0.243

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 1BYU	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1QG2 CANINE GDP-RAN R76E MUTANT Deposited 1999-04-20	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 1–216（216 aa） Fragment：ALL	Mutation：R76E	MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.2；SEE PUBLICATION, pH 7.20	Resolution 2.50 Å R-free 0.237
1QG4 CANINE GDP-RAN F72Y MUTANT Deposited 1999-04-20	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 1–216（216 aa） Fragment：ALL	Mutation：F72Y	MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.2；pH 7.20	Resolution 2.50 Å R-free 0.237
1QG4 CANINE GDP-RAN F72Y MUTANT Deposited 1999-04-20	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 1–216（216 aa） Fragment：ALL	Mutation：F72Y	MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.2；pH 7.20	Resolution 2.50 Å R-free 0.237
1WA5 Structure of the Cse1:Imp-alpha:RanGTP complex Deposited 2004-10-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–176（176 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；291 K；50mM TrisHCl, 200mM NaCl, 5mM Mg(OAc)2, .1mM GTP, 22% PEG3350 and 2% PEG400.	Resolution 2.00 Å R-free 0.216
2BKU Kap95p:RanGTP complex Deposited 2005-02-21	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 1–177（177 aa） Fragment：RESIDUES 1-177	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.70 Å R-free 0.279
2BKU Kap95p:RanGTP complex Deposited 2005-02-21	Different construct Different mutation/modification 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 1–177（177 aa） Fragment：RESIDUES 1-177	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.70 Å R-free 0.279
3A6P Crystal structure of Exportin-5:RanGTP:pre-miRNA complex Deposited 2009-09-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain C 1–216（216 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.92 Å R-free 0.312
3A6P Crystal structure of Exportin-5:RanGTP:pre-miRNA complex Deposited 2009-09-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–RNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain H 1–216（216 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.92 Å R-free 0.312
3RAN CANINE GDP-RAN Q69L MUTANT Deposited 1998-10-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–216（216 aa）	Mutation：Q69L	MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.2；SEE PUBLICATION, pH 7.2	Resolution 2.15 Å R-free 0.243
3RAN CANINE GDP-RAN Q69L MUTANT Deposited 1998-10-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–216（216 aa）	Mutation：Q69L	MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.2；SEE PUBLICATION, pH 7.2	Resolution 2.15 Å R-free 0.243
3RAN CANINE GDP-RAN Q69L MUTANT Deposited 1998-10-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–216（216 aa）	Mutation：Q69L	MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.2；SEE PUBLICATION, pH 7.2	Resolution 2.15 Å R-free 0.243
3RAN CANINE GDP-RAN Q69L MUTANT Deposited 1998-10-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1–216（216 aa）	Mutation：Q69L	MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.2；SEE PUBLICATION, pH 7.2	Resolution 2.15 Å R-free 0.243
3W3Z Crystal structure of Kap121p bound to RanGTP Deposited 2012-12-28	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 B 1–176（176 aa） Fragment：UNP residues 1-176	Not recorded	MG MAGNESIUM ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1M MES, 0.2M CaCl2, 10% PEG 20000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.70 Å R-free 0.298
5BXQ Structure of the NTF2:RanGDP complex Deposited 2015-06-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 1–216（216 aa） Chain D 1–216（216 aa） Chain E 1–216（216 aa）	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 3 MG MAGNESIUM ION × 3 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M Li2SO4, 50 mM Na Citrate pH5.6, 15% PEG4000	Resolution 2.50 Å R-free 0.225
5YU6 CRYSTAL STRUCTURE OF EXPORTIN-5:RANGTP COMPLEX Deposited 2017-11-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–216（216 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG3350, DTT, MgCl2, spermine tetrahydrochloride	Resolution 3.00 Å R-free 0.269
5YU6 CRYSTAL STRUCTURE OF EXPORTIN-5:RANGTP COMPLEX Deposited 2017-11-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–216（216 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG3350, DTT, MgCl2, spermine tetrahydrochloride	Resolution 3.00 Å R-free 0.269

9 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RAN_CANFA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–216； UniProt 1–216 Author chain B； PDBConstruct 1–216； UniProt 1–216

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	1byu
Deposition date deposition_date	1998-10-18
Structure title title	CANINE GDP-RAN
Keywords keywords	GTPASE, NUCLEAR TRANSPORT, TRANSPORT PROTEIN; TRANSPORT 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	25.83 Å
Radius of gyration Rg (electron density) rg_electron	24.98 Å
Forward intensity I(0) i0	38072300.00
Molecular weight molecular_weight	48192.0 kDa
Excluded volume excluded_volume	60623 Å³
Envelope volume envelope_volume	77800 Å³
Hydration-shell volume shell_volume	26563 Å³
Envelope diameter envelope_diameter	88.1 Å
Shell Rg shell_rg	31.64 Å
Envelope Rg envelope_rg	24.71 Å
Shape Rg shape_rg	24.96 Å
Total Rg total_rg	25.84 Å
Total atoms total_atoms	3397
Residues n_residues	417
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	84.0 Å
Rg (real space) rg_real	25.84 Å
Rg uncertainty (real space) rg_real_error	0.59 Å
I(0) (real space) i0_real	3.8070e+07
I(0) uncertainty (real space) i0_real_error	5.8960e+05
Rg (reciprocal space) rg_reciprocal	25.84 Å
I(0) (reciprocal space) i0_reciprocal	38070000.0000
Solution quality estimate total_estimate	0.8952
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.5 Å
Skewness Skewness skewness	0.335
Kurtosis Kurtosis kurtosis	-0.490
Angular range angular_range	— – 0.3050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7738000.0000
Real-space data points n_real_points	62
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.885; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.997

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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 (GTP-BINDING PROTEIN RAN)
Molecular weight formula_weight	24482.1 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	3594

MAAQGEPQVQFKLVLVGDGGTGKTTFVKRHLTGEFEKKYVPTLGVEVHPLVFHTNRGPIKFNVWDTAGQEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLCGNKVDIKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMPALAPPEVVMDPALAAQYEHDLEVAQTTALPDEDDDL

来源 Source

来源生物 organism	Canis lupus familiaris
通用名 common_name	dog
NCBI Class编号 ncbi_taxonomy_id	9615
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	2

Entity 3 Entity 3 non-polymer

Description description	GUANOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	443.2 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	197

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1byua_
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	d1byub_
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	1byuA00
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	1byuB00
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	60.790 Å
Unit-cell length b length_b	60.433 Å
Unit-cell length c length_c	61.200 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	101.67 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.150 Å
Low-resolution limit resolution_low	6.000 Å
R factor r_factor	—
R_work r_work	0.1760
R_free r_free	0.2430

fit	/app/data/saxs_computation/by/1byu/1byu.fit
pddf	/app/data/pr_computation/by/1byu/1byu.pr.out
profile	/app/data/saxs_computation/by/1byu/1byu.dat

CANINE GDP-RAN

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

PROTEIN (GTP-BINDING PROTEIN RAN)

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