SAXSdb — 5ji9

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

Ran-binding protein 9

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 108–350	Fragment：IUS-SPRY DOMAIN, UNP RESIDUES 108-350	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；0.1M NA-CACODYLATE, PH 6.5, 6% PEG 4000, 0.2M KCL, 0.02M MGCL2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K	Resolution 2.50 Å R-free 0.227

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 5JI9	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5JI7 The Crystal Structure Of IUS-SPRY Domain From RanBPM/9 Deposited 2016-04-22	Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 108–350（243 aa） Fragment：IUS-SPRY DOMAIN, UNP RESIDUES 108-350	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；0.1M NA-CACODYLATE, PH 6.5, 6% PEG 4000, 0.2M KCL, 0.02M MGCL2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K	Resolution 1.51 Å R-free 0.191
5JIU The crystal structure of RanBPM/9 IUS-SPRY domain in complex with DDX-4 peptide Deposited 2016-04-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 108–350（243 aa） Fragment：UNP RESIDUES 108-350 Chain B 108–350（243 aa） Fragment：UNP RESIDUES 108-350	Not recorded	CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；20~25% (w/v) PEG 3350, 0.1 M Bis-Tris, pH 6.5, 0.2 M NaCl	Resolution 2.05 Å R-free 0.203
7NSC Substrate receptor scaffolding module of human CTLH E3 ubiquitin ligase Deposited 2021-03-05	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–729（729 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å

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

View Construct and Data Evidence

UniProt name	RANB9_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–243； UniProt 108–350

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	5ji9
Deposition date deposition_date	2016-04-22
Structure title title	The Crystal Structure Of IUS-SPRY Domain From RanBPM/9
Keywords keywords	BETA SANDWICH, TRANSPORT PROTEIN, RAN-BINDING PROTEIN; RAN-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	17.17 Å
Radius of gyration Rg (electron density) rg_electron	15.90 Å
Forward intensity I(0) i0	9901540.00
Molecular weight molecular_weight	22833.0 kDa
Excluded volume excluded_volume	28312 Å³
Envelope volume envelope_volume	31191 Å³
Hydration-shell volume shell_volume	16202 Å³
Envelope diameter envelope_diameter	54.0 Å
Shell Rg shell_rg	22.25 Å
Envelope Rg envelope_rg	16.29 Å
Shape Rg shape_rg	15.88 Å
Total Rg total_rg	16.99 Å
Total atoms total_atoms	1612
Residues n_residues	205
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	55.2 Å
Rg (real space) rg_real	17.05 Å
Rg uncertainty (real space) rg_real_error	0.27 Å
I(0) (real space) i0_real	9.9020e+06
I(0) uncertainty (real space) i0_real_error	1.1510e+05
Rg (reciprocal space) rg_reciprocal	17.07 Å
I(0) (reciprocal space) i0_reciprocal	9902000.0000
Solution quality estimate total_estimate	0.7137
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	22.5 Å
Skewness Skewness skewness	0.145
Kurtosis Kurtosis kurtosis	-0.373
Angular range angular_range	— – 0.4650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2759000.0000
Real-space data points n_real_points	77
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.838; Stabil: 1.000; Sysdev: 0.257; Positv: 1.000; Valcen: 0.994; Smooth: 0.992

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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) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	5ji9A00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	920 — SPRY domain

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8. Citations (1)

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Unit-cell length a length_a	69.478 Å
Unit-cell length b length_b	69.478 Å
Unit-cell length c length_c	107.688 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 65
Space-group number int_tables_number	170
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	40.120 Å
R factor r_factor	0.1730
R_work r_work	0.1670
R_free r_free	0.2270

Description description	Ran-binding protein 9
Molecular weight formula_weight	26344.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1667

The Crystal Structure Of IUS-SPRY Domain From RanBPM/9

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

Ran-binding protein 9

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) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	55

fit	/app/data/saxs_computation/ji/5ji9/5ji9.fit
pddf	/app/data/pr_computation/ji/5ji9/5ji9.pr.out
profile	/app/data/saxs_computation/ji/5ji9/5ji9.dat