SAXSdb — 6kzf

▼

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

Kunitz-type serine protease inhibitor homolog calcicludine

OrganismNot specified

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 1–60	Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Ammonium acetate, 0.1M Sodium citrate tribasic dihydrate pH 5.6, 30% w/v Polyethylene glycol 4000	Resolution 2.52 Å R-free 0.282

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 6KZF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BF0 CALCICLUDINE (CAC) FROM GREEN MAMBA DENDROASPIS ANGUSTICEPS, NMR, 15 STRUCTURES Deposited 1998-05-26	Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–60（60 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4.5；30 K	Resolution not provided
5YV7 Racemic X-ray Structure of Calcicludine Deposited 2017-11-24	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–60（60 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；sodium citrate tribasic dihydrate, 20% w/v polyethylene glycol 3350	Resolution 2.40 Å R-free 0.302

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

View Construct and Data Evidence

UniProt name	VKTHC_DENAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–60； UniProt 1–60

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	6kzf
Deposition date deposition_date	2019-09-24
Structure title title	Racemic X-ray Structure of Calcicludine
Keywords keywords	calcicludine, racemic crystal, L-type Ca2+ channels, TOXIN; TOXIN
Experimental Method method	X-RAY DIFFRACTION

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	18.46 Å
Radius of gyration Rg (electron density) rg_electron	17.95 Å
Forward intensity I(0) i0	3400350.00
Molecular weight molecular_weight	14022.0 kDa
Excluded volume excluded_volume	17959 Å³
Envelope volume envelope_volume	21017 Å³
Hydration-shell volume shell_volume	10916 Å³
Envelope diameter envelope_diameter	63.0 Å
Shell Rg shell_rg	22.08 Å
Envelope Rg envelope_rg	18.34 Å
Shape Rg shape_rg	17.87 Å
Total Rg total_rg	18.99 Å
Total atoms total_atoms	982
Residues n_residues	65
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

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	64.9 Å
Rg (real space) rg_real	18.64 Å
Rg uncertainty (real space) rg_real_error	0.56 Å
I(0) (real space) i0_real	3.4000e+06
I(0) uncertainty (real space) i0_real_error	4.3620e+04
Rg (reciprocal space) rg_reciprocal	18.61 Å
I(0) (reciprocal space) i0_reciprocal	3400000.0000
Solution quality estimate total_estimate	0.8205
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	15.1 Å
Skewness Skewness skewness	0.485
Kurtosis Kurtosis kurtosis	-0.434
Angular range angular_range	— – 0.4300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	728900.0000
Real-space data points n_real_points	74
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.742; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.495; Smooth: 0.944

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Kunitz-type serine protease inhibitor homolog calcicludine
Molecular weight formula_weight	6980.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1043

WQPPWYAKEPVRIGSCKKQFSSFYFKWTAKKCLPFLFSGCGGNANRFQTIGECRKKCLGK

Entity 2 Entity 2 polymer

Description description	D-calcicludine
Molecular weight formula_weight	6989.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(D)
Chain IDs strand_id	B

WQPPWYCKEPVRIGSCKKQFSSFYFKWTAKKCLPFLFSGCGGNANRFQTIGECRKKCLGK

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	61

▼

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	6kzfA00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	410 — Factor Xa Inhibitor
Homologous superfamily homologous superfamily	10 — Pancreatic trypsin inhibitor Kunitz domain

▶

8. Citations (1)

▶

Unit-cell length a length_a	94.600 Å
Unit-cell length b length_b	94.600 Å
Unit-cell length c length_c	38.562 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	I 41
Space-group number int_tables_number	80
Crystal system crystal_system	—

Resolution resolution	2.520 Å
Low-resolution limit resolution_low	35.710 Å
R factor r_factor	—
R_work r_work	0.2389
R_free r_free	0.2821

fit	/app/data/saxs_computation/kz/6kzf/6kzf.fit
pddf	/app/data/pr_computation/kz/6kzf/6kzf.pr.out
profile	/app/data/saxs_computation/kz/6kzf/6kzf.dat

Racemic X-ray Structure of Calcicludine

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

Kunitz-type serine protease inhibitor homolog calcicludine

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 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)