SAXSdb — 1jhn

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

calnexin

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 45–468	Fragment：lumenal domain (residues 45-468)	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；HEPES, MPD, Calcium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.90 Å R-free 0.377

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 1JHN	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8RJC Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in complex with Sec61-TRAP, open conformation 1 Deposited 2023-12-20	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 56-meric	Chain 9 1–593（593 aa）	Not recorded	MG MAGNESIUM ION × 218 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
8RJD Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in complex with Sec61-TRAP, open conformation 2 Deposited 2023-12-20	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 56-meric	Chain 9 1–593（593 aa）	Not recorded	MG MAGNESIUM ION × 218 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.79 Å

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

View Construct and Data Evidence

UniProt name	CALX_CANFA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–424； UniProt 45–468

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	1jhn
Deposition date deposition_date	2001-06-28
Structure title title	Crystal Structure of the Lumenal Domain of Calnexin
Keywords keywords	jelly-roll, beta sandwich, CHAPERONE; CHAPERONE
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	34.30 Å
Radius of gyration Rg (electron density) rg_electron	33.75 Å
Forward intensity I(0) i0	28215000.00
Molecular weight molecular_weight	40304.0 kDa
Excluded volume excluded_volume	49720 Å³
Envelope volume envelope_volume	85994 Å³
Hydration-shell volume shell_volume	22881 Å³
Envelope diameter envelope_diameter	102.8 Å
Shell Rg shell_rg	37.62 Å
Envelope Rg envelope_rg	32.91 Å
Shape Rg shape_rg	33.75 Å
Total Rg total_rg	34.16 Å
Total atoms total_atoms	2854
Residues n_residues	380
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	106.4 Å
Rg (real space) rg_real	34.44 Å
Rg uncertainty (real space) rg_real_error	1.17 Å
I(0) (real space) i0_real	2.8210e+07
I(0) uncertainty (real space) i0_real_error	4.5430e+05
Rg (reciprocal space) rg_reciprocal	34.36 Å
I(0) (reciprocal space) i0_reciprocal	28210000.0000
Solution quality estimate total_estimate	0.7693
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.4 Å
Skewness Skewness skewness	0.164
Kurtosis Kurtosis kurtosis	-1.118
Angular range angular_range	— – 0.2300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2308000.0000
Real-space data points n_real_points	47
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.488; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.616; Smooth: 0.920

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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	d1jhna3
Class class	b — All beta proteins
Fold Fold fold	b.104 — P-domain of calnexin/calreticulin
Superfamily Superfamily superfamily	b.104.1 — P-domain of calnexin/calreticulin
Family Family family	b.104.1.1 — P-domain of calnexin/calreticulin

Domain ID domain_id	d1jhna4
Class class	b — All beta proteins
Fold Fold fold	b.29 — Concanavalin A-like lectins/glucanases
Superfamily Superfamily superfamily	b.29.1 — Concanavalin A-like lectins/glucanases
Family Family family	b.29.1.12 — Calnexin/calreticulin

CATH v4.4 (2 domains)

Domain ID domain_id	1jhnA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	1jhnA02
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	250 — Calnexin lumenal domain, non-globular proline-rich hairpin domain
Homologous superfamily homologous superfamily	10 — Calreticulin/calnexin, P domain

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8. Citations (2)

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Unit-cell length a length_a	85.772 Å
Unit-cell length b length_b	85.772 Å
Unit-cell length c length_c	143.476 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	8

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	33.800 Å
R factor r_factor	—
R_work r_work	0.3270
R_free r_free	0.3770

Description description	calnexin
Molecular weight formula_weight	48291.8 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	2854

Crystal Structure of the Lumenal Domain of Calnexin

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

calnexin

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 non-polymer

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)

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	Spodoptera frugiperda

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

fit	/app/data/saxs_computation/jh/1jhn/1jhn.fit
pddf	/app/data/pr_computation/jh/1jhn/1jhn.pr.out
profile	/app/data/saxs_computation/jh/1jhn/1jhn.dat