SAXSdb — 2qfe

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

Calpain-7

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 684–813	Fragment：Distal C2-Like Domain	BR BROMIDE ION × 18	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；The crystals were grown in 1.4 M NaKPO4 pH 7.0, by mixing equal volumes of the precipitant solution and 13 mg/mL protein in binding buffer (500 mM NaCl, 50 mM Tris pH 8.0). The crystal was soaked for 1 hour in a solution containing 2 M NaBr., VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.45 Å R-free 0.215

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 2QFE	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8UC6 Calpain-7:IST1 Complex Deposited 2023-09-25	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–165（165 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.2；294 K；Both proteins were purified and concentrated to 20 mg/ml in buffer containing 25 mM Tris, pH 7.2, 150 mM NaCl, 1 mM TCEP, 0.5 mM EDTA. The proteins were mixed in a 1:2 molar ratio (CAPN7:IST1). Crystals grew at 21 C (294 K) in Rigaku Wizard Cryo condition D5 (25% (v/v) 1,2-Porpanediol, 100 mM Sodium phosphate dibasic/Citric acid pH 4.2, 5% (w/v) PEG 3000, 10% (v/v) Glycerol. Crystals were transferred briefly to crystallization buffer supplemented with 25% added glycerol prior to plunging in liquid nitrogen	Resolution 2.70 Å R-free 0.285
8UC6 Calpain-7:IST1 Complex Deposited 2023-09-25	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–165（165 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.2；294 K；Both proteins were purified and concentrated to 20 mg/ml in buffer containing 25 mM Tris, pH 7.2, 150 mM NaCl, 1 mM TCEP, 0.5 mM EDTA. The proteins were mixed in a 1:2 molar ratio (CAPN7:IST1). Crystals grew at 21 C (294 K) in Rigaku Wizard Cryo condition D5 (25% (v/v) 1,2-Porpanediol, 100 mM Sodium phosphate dibasic/Citric acid pH 4.2, 5% (w/v) PEG 3000, 10% (v/v) Glycerol. Crystals were transferred briefly to crystallization buffer supplemented with 25% added glycerol prior to plunging in liquid nitrogen	Resolution 2.70 Å R-free 0.285

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

View Construct and Data Evidence

UniProt name	CAN7_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 19–148； UniProt 684–813

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	2qfe
Deposition date deposition_date	2007-06-27
Structure title title	Distal C2-Like Domain of Human Calpain-7
Keywords keywords	C2-Like Domain, Hydrolase; Nuclear protein; Protease; Thiol Protease, 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	15.68 Å
Radius of gyration Rg (electron density) rg_electron	14.56 Å
Forward intensity I(0) i0	6549080.00
Molecular weight molecular_weight	16682.0 kDa
Excluded volume excluded_volume	19728 Å³
Envelope volume envelope_volume	22334 Å³
Hydration-shell volume shell_volume	13039 Å³
Envelope diameter envelope_diameter	50.2 Å
Shell Rg shell_rg	20.35 Å
Envelope Rg envelope_rg	14.91 Å
Shape Rg shape_rg	14.47 Å
Total Rg total_rg	15.75 Å
Total atoms total_atoms	1097
Residues n_residues	139
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	50.8 Å
Rg (real space) rg_real	15.57 Å
Rg uncertainty (real space) rg_real_error	0.26 Å
I(0) (real space) i0_real	6.5490e+06
I(0) uncertainty (real space) i0_real_error	7.4930e+04
Rg (reciprocal space) rg_reciprocal	15.58 Å
I(0) (reciprocal space) i0_reciprocal	6549000.0000
Solution quality estimate total_estimate	0.8818
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	20.6 Å
Skewness Skewness skewness	0.128
Kurtosis Kurtosis kurtosis	-0.325
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1021000.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.822; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.996

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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	Calpain-7
Molecular weight formula_weight	16456.6 kDa
EC 编号 ec_number	3.4.22.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1314

MGSSHHHHHHSSGLVPRGSPYTLSKRINGKWSGQSAGGCGNFQETHKNNPIYQFHIEKTGPLLIELRGPRQYSVGFEVVTVSTLGDPGPHGFLRKSSGDYRCGFCYLELENIPSGIFNIIPSTFLPKQEGPFFLDFNSIIPIKITQLQ

来源 Source

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 BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	BROMIDE ION
Molecular weight formula_weight	79.9 kDa
Source method src_method	syn
Copy count entity_count	18

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	181

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	2qfeA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	380 —

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8. Citations (1)

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Unit-cell length a length_a	57.513 Å
Unit-cell length b length_b	57.513 Å
Unit-cell length c length_c	88.676 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 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	1.450 Å
Low-resolution limit resolution_low	29.990 Å
R factor r_factor	0.1885
R_work r_work	0.1871
R_free r_free	0.2154

fit	/app/data/saxs_computation/qf/2qfe/2qfe.fit
pddf	/app/data/pr_computation/qf/2qfe/2qfe.pr.out
profile	/app/data/saxs_computation/qf/2qfe/2qfe.dat

Distal C2-Like Domain of Human Calpain-7

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

Calpain-7

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