SAXSdb — 1np8

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

Calcium-dependent protease, small subunit

Rattus norvegicus

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 87–245 Chain B； UniProt 87–245	Fragment：residues 87-245	CD CADMIUM ION × 13	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.6；294 K；PEG, cadmium chloride, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.00 Å R-free 0.239

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 1NP8	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AJ5 CALPAIN DOMAIN VI APO Deposited 1997-05-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 12–184（173 aa） Fragment：SMALL REGULATORY SUBUNIT, DOMAIN VI, MET 87 - SER 270	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.8；38%SATURATED AMMONIUM SULFATE AND 25MM PIPES BUFFER, PH 6.8	Resolution 2.30 Å R-free 0.306
1AJ5 CALPAIN DOMAIN VI APO Deposited 1997-05-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 12–184（173 aa） Fragment：SMALL REGULATORY SUBUNIT, DOMAIN VI, MET 87 - SER 270	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.8；38%SATURATED AMMONIUM SULFATE AND 25MM PIPES BUFFER, PH 6.8	Resolution 2.30 Å R-free 0.306
1DF0 Crystal structure of M-Calpain Deposited 1999-11-16	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 1–184（184 aa） Fragment：DOMAIN VI (CALCIUM-BINDING DOMAIN), SMALL (REGULATORY) SUBUNIT	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.25；298 K；PEG 6000, MES, SODIUM CHLORIDE, DITHIOTHREITOL, EDTA, pH 6.25, VAPOR DIFFUSION, HANGING DROP	Resolution 2.60 Å R-free 0.293
1DVI CALPAIN DOMAIN VI WITH CALCIUM BOUND Deposited 1997-05-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–184（184 aa） Fragment：SMALL (REGULATORY) SUBUNIT, DOMAIN VI, RESIDUES 87 - 270 Chain B 1–184（184 aa） Fragment：SMALL (REGULATORY) SUBUNIT, DOMAIN VI, RESIDUES 87 - 270	Not recorded	CA CALCIUM ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；17% PEG 8K, 50MM CACODYLATE PH. 6.5 , 10% GLYCEROL, 200MM CACL2	Resolution 2.30 Å R-free 0.294
1U5I Crystal Structure analysis of rat m-calpain mutant Lys10 Thr Deposited 2004-07-27	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 84–266（183 aa） Fragment：residues 1-184	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；298 K；PEG 6000, MES, sodium chloride, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.86 Å R-free 0.283
3BOW Structure of M-calpain in complex with Calpastatin Deposited 2007-12-17	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 88–270（183 aa） Fragment：UNP residues 88-270	Not recorded	CA CALCIUM ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；298 K；pH 6.5, microbatch under paraffin oil, temperature 298K	Resolution 2.40 Å R-free 0.258
3DF0 Calcium-dependent complex between m-calpain and calpastatin Deposited 2008-06-11	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 87–270（184 aa） Fragment：UNP residues 87-270	Not recorded	CA CALCIUM ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；4-9% PEG 3350, 5-10 mM CaCl2, 50-100 mM NaOAc (pH 5.5) , VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.95 Å R-free 0.299

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

View Construct and Data Evidence

UniProt name	CPNS1_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–159； UniProt 87–245 Author chain B； PDBConstruct 1–159； UniProt 87–245

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	1np8
Deposition date deposition_date	2003-01-17
Structure title title	18-k C-terminally trunucated small subunit of calpain
Keywords keywords	dimer in solution, oligomer in crystal, HYDROLASE; HYDROLASE
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	21.65 Å
Radius of gyration Rg (electron density) rg_electron	20.65 Å
Forward intensity I(0) i0	25522600.00
Molecular weight molecular_weight	35790.0 kDa
Excluded volume excluded_volume	43169 Å³
Envelope volume envelope_volume	51611 Å³
Hydration-shell volume shell_volume	21055 Å³
Envelope diameter envelope_diameter	72.5 Å
Shell Rg shell_rg	27.08 Å
Envelope Rg envelope_rg	20.95 Å
Shape Rg shape_rg	20.65 Å
Total Rg total_rg	21.43 Å
Total atoms total_atoms	2425
Residues n_residues	298
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	70.2 Å
Rg (real space) rg_real	21.59 Å
Rg uncertainty (real space) rg_real_error	0.43 Å
I(0) (real space) i0_real	2.5520e+07
I(0) uncertainty (real space) i0_real_error	3.2560e+05
Rg (reciprocal space) rg_reciprocal	21.60 Å
I(0) (reciprocal space) i0_reciprocal	25520000.0000
Solution quality estimate total_estimate	0.8916
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.2 Å
Skewness Skewness skewness	0.268
Kurtosis Kurtosis kurtosis	-0.370
Angular range angular_range	— – 0.3650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3122000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.874; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.969

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Calcium-dependent protease, small subunit
Molecular weight formula_weight	18350.6 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	2649

NIEANESEEERQFRKLFVQLAGDDMEVSATELMNILNKVVTRHPDLKTDGFGIDTCRSMVAVMDSDTTGKLGFEEFKYLWNNIKKWQGIYKRFDTDRSGTIGSNELPGAFEAAGFHLNQHIYSMIIRRYSDETGNMDFDNFISCLVRLDAMFRAFRSLD

来源 Source

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

Entity 2 Entity 2 non-polymer

Description description	CADMIUM ION
Molecular weight formula_weight	112.4 kDa
Source method src_method	syn
Copy count entity_count	13

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	224

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1np8a_
Class class	a — All alpha proteins
Fold Fold fold	a.39 — EF Hand-like
Superfamily Superfamily superfamily	a.39.1 — EF-hand
Family Family family	a.39.1.8 — Penta-EF-hand proteins

Domain ID domain_id	d1np8b_
Class class	a — All alpha proteins
Fold Fold fold	a.39 — EF Hand-like
Superfamily Superfamily superfamily	a.39.1 — EF-hand
Family Family family	a.39.1.8 — Penta-EF-hand proteins

CATH v4.4 (2 domains)

Domain ID domain_id	1np8A00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

Domain ID domain_id	1np8B00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

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8. Citations (1)

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Unit-cell length a length_a	58.040 Å
Unit-cell length b length_b	67.570 Å
Unit-cell length c length_c	75.070 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 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.1960
R_work r_work	0.1960
R_free r_free	0.2390

fit	/app/data/saxs_computation/np/1np8/1np8.fit
pddf	/app/data/pr_computation/np/1np8/1np8.pr.out
profile	/app/data/saxs_computation/np/1np8/1np8.dat

18-k C-terminally trunucated small subunit of calpain

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

Calcium-dependent protease, small subunit

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