SAXSdb — 1jb5

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

NUCLEAR TRANSPORT FACTOR 2

Rattus norvegicus

UniProt P61972

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 1–127 Chain B； UniProt 1–127	Mutation：M118E	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.5；291 K；PEG, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.30 Å R-free 0.289

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 1JB5	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AR0 NUCLEAR TRANSPORT FACTOR 2 (NTF2) E42K MUTANT Deposited 1997-08-08	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–127（127 aa） Chain B 1–127（127 aa）	Mutation：E42K Mutation：E42K	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；pH 4.5	Resolution 2.30 Å R-free 0.228
1ASK NUCLEAR TRANSPORT FACTOR 2 (NTF2) H66A MUTANT Deposited 1997-08-11	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–127（127 aa） Chain B 1–127（127 aa）	Mutation：H66A Mutation：H66A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；pH 4.5	Resolution 2.30 Å R-free 0.243
1JB2 CRYSTAL STRUCTURE OF NTF2 M84E MUTANT Deposited 2001-06-01	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–127（127 aa） Chain B 1–127（127 aa）	Mutation：M84E Mutation：M84E	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；PEG, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.00 Å R-free 0.251
1JB4 CRYSTAL STRUCTURE OF NTF2 M102E MUTANT Deposited 2001-06-01	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–127（127 aa） Chain B 1–127（127 aa）	Mutation：M102E Mutation：M102E	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；PEG, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.23 Å R-free 0.241
1OUN CRYSTAL STRUCTURE OF NUCLEAR TRANSPORT FACTOR 2 (NTF2) Deposited 1996-02-21	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–127（127 aa） Chain B 1–127（127 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；pH 4.5	Resolution 2.30 Å R-free 0.230
1U5O Structure of the D23A mutant of the nuclear transport carrier NTF2 Deposited 2004-07-28	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–127（127 aa） Chain B 1–127（127 aa）	Mutation：D23A Mutation：D23A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.7；298 K；PEG 8000, magnesium acetate, sodium acetate, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.50 Å R-free 0.261
5BXQ Structure of the NTF2:RanGDP complex Deposited 2015-06-09	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 A 1–127（127 aa） Chain B 1–127（127 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

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NTF2_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–127； UniProt 1–127 Author chain B； PDBConstruct 1–127； UniProt 1–127

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	1jb5
Deposition date deposition_date	2001-06-01
Structure title title	CRYSTAL STRUCTURE OF NTF2 M118E MUTANT
Keywords keywords	NTF2, Transport, PROTEIN TRANSPORT; PROTEIN TRANSPORT
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	18.76 Å
Radius of gyration Rg (electron density) rg_electron	17.59 Å
Forward intensity I(0) i0	14020700.00
Molecular weight molecular_weight	28158.0 kDa
Excluded volume excluded_volume	35223 Å³
Envelope volume envelope_volume	39733 Å³
Hydration-shell volume shell_volume	18600 Å³
Envelope diameter envelope_diameter	61.2 Å
Shell Rg shell_rg	24.20 Å
Envelope Rg envelope_rg	18.05 Å
Shape Rg shape_rg	17.59 Å
Total Rg total_rg	18.60 Å
Total atoms total_atoms	1986
Residues n_residues	246
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	60.5 Å
Rg (real space) rg_real	18.68 Å
Rg uncertainty (real space) rg_real_error	0.28 Å
I(0) (real space) i0_real	1.4020e+07
I(0) uncertainty (real space) i0_real_error	1.4910e+05
Rg (reciprocal space) rg_reciprocal	18.69 Å
I(0) (reciprocal space) i0_reciprocal	14020000.0000
Solution quality estimate total_estimate	0.8833
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.2 Å
Skewness Skewness skewness	0.253
Kurtosis Kurtosis kurtosis	-0.309
Angular range angular_range	— – 0.4250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3986000.0000
Real-space data points n_real_points	74
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.840; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.961

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1jb5a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.17 — Cystatin-like
Superfamily Superfamily superfamily	d.17.4 — NTF2-like
Family Family family	d.17.4.2 — NTF2-like

Domain ID domain_id	d1jb5b_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.17 — Cystatin-like
Superfamily Superfamily superfamily	d.17.4 — NTF2-like
Family Family family	d.17.4.2 — NTF2-like

CATH v4.4 (2 domains)

Domain ID domain_id	1jb5A00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	1jb5B00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	50 —

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8. Citations (1)

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Unit-cell length a length_a	34.680 Å
Unit-cell length b length_b	78.210 Å
Unit-cell length c length_c	41.430 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	104.55 °
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	2.300 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2030
R_work r_work	0.2030
R_free r_free	0.2890

Description description	NUCLEAR TRANSPORT FACTOR 2
Molecular weight formula_weight	14475.3 kDa
Mutation mutation	M118E
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2098

CRYSTAL STRUCTURE OF NTF2 M118E MUTANT

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

NUCLEAR TRANSPORT FACTOR 2

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	112

fit	/app/data/saxs_computation/jb/1jb5/1jb5.fit
pddf	/app/data/pr_computation/jb/1jb5/1jb5.pr.out
profile	/app/data/saxs_computation/jb/1jb5/1jb5.dat