SAXSdb — 1df0

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1. Structure Basics

entry_id	1df0
deposition_date	1999-11-16
title	Crystal structure of M-Calpain
keywords	CYSTEINE PROTEASE, CALMODULIN, PAPAIN, CATALYTIC TRIAD, ZYMOGEN ACTIVATION, C2 DOMAIN, PROTEASE, ZYMOGEN, CALPAIN, HYDROLASE; HYDROLASE
method	X-RAY DIFFRACTION

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	31.46 Å
rg_electron	30.78 Å
i0	130394000.00
molecular_weight	90684.0 kDa
excluded_volume	113370 Å³
envelope_volume	144060 Å³
shell_volume	39120 Å³
envelope_diameter	110.6 Å
shell_rg	37.68 Å
envelope_rg	30.75 Å
shape_rg	30.80 Å
total_rg	31.34 Å
total_atoms	6391
n_residues	800
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	105.4 Å
rg_real	31.50 Å
rg_real_error	0.63 Å
i0_real	1.3040e+08
i0_real_error	1.7610e+06
rg_reciprocal	31.49 Å
i0_reciprocal	130400000.0000
total_estimate	0.8810
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	33.7 Å
skewness	0.409
kurtosis	-0.271
angular_range	— – 0.2500 Å⁻¹
current_alpha	0.0000
highest_alpha	33420000.0000
n_real_points	51
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.841; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.930

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	M-CALPAIN
formula_weight	79994.0 kDa
ec_number	3.4.22.53
mutation	C105S
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	6749

MAGIAMKLAKDREAAEGLGSHERAIKYLNQDYETLRNECLEAGALFQDPSFPALPSSLGFKELGPYSSKTRGIEWKRPTEICADPQFIIGGATRTDICQGALGDSWLLAAIASLTLNEEILARVVPLDQSFQENYAGIFHFQFWQYGEWVEVVVDDRLPTKDGELLFVHSAEGSEFWSALLEKAYAKINGCYEALSGGATTEGFEDFTGGIAEWYELRKPPPNLFKIIQKALEKGSLLGCSIDITSAADSEAVTYQKLVKGHAYSVTGAEEVESSGSLQKLIRIRNPWGQVEWTGKWNDNCPSWNTVDPEVRANLTERQEDGEFWMSFSDFLRHYSRLEICNLTPDTLTCDSYKKWKLTKMDGNWRRGSTAGGCRNYPNTFWMNPQYLIKLEEEDEDDEDGERGCTFLVGLIQKHRRRQRKMGEDMHTIGFGIYEVPEELTGQTNIHLSKNFFLTTRARERSDTFINLREVLNRFKLPPGEYVLVPSTFEPHKNGDFCIRVFSEKKADYQTVDDEIEANIEEIEANEEDIGDGFRRLFAQLAGEDAEISAFELQTILRRVLAKREDIKSDGFSIETCKIMVDMLDEDGSGKLGLKEFYILWTKIQKYQKIYREIDVDRSGTMNSYEMRKALEEAGFKLPCQLHQVIVARFADDELIIDFDNFVRCLVRLEILFKIFKQLDPENTGTIQLDLISWLSFSVL

Source

organism	Rattus norvegicus
common_name	Norway rat
ncbi_taxonomy_id	10116
host_organism	Escherichia coli

Entity 2 polymer

description	CALPAIN
formula_weight	21305.0 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MHYSNIEANESEEERQFRKLFVQLAGDDMEVSATELMNILNKVVTRHPDLKTDGFGIDTCRSMVAVMDSDTTGKLGFEEFKYLWNNIKKWQGIYKRFDTDRSGTIGSNELPGAFEAAGFHLNQHIYSMIIRRYSDETGNMDFDNFISCLVRLDAMFRAFRSLDKNGTGQIQVNIQEWLQLTMYS

Source

organism	Rattus norvegicus
common_name	Norway rat
ncbi_taxonomy_id	10116
host_organism	Escherichia coli

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	358

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6. Citations (4)

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length_a	57.696 Å
length_b	80.181 Å
length_c	80.720 Å
angle_alpha	60.37 °
angle_beta	70.85 °
angle_gamma	79.49 °
z_pdb	1

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	2.600 Å
resolution_low	25.000 Å
r_factor	0.2230
r_work	0.2230
r_free	0.2930

fit	/app/data/saxs_computation/df/1df0/1df0.fit
pddf	/app/data/pr_computation/df/1df0/1df0.pr.out
profile	/app/data/saxs_computation/df/1df0/1df0.dat

Crystal structure of M-Calpain

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction

5. Entities & Polymer Info (3)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 water

6. Citations (4)

7. Files & Curves (10)

Files (7)

Curves (3)