← Back to search

1cqd

THE 2.1 ANGSTROM STRUCTURE OF A CYSTEINE PROTEASE WITH PROLINE SPECIFICITY FROM GINGER RHIZOME, ZINGIBER OFFICINALE

Method: X-RAY DIFFRACTION D_max: 108.5 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	1cqd
deposition_date	1999-06-15
title	THE 2.1 ANGSTROM STRUCTURE OF A CYSTEINE PROTEASE WITH PROLINE SPECIFICITY FROM GINGER RHIZOME, ZINGIBER OFFICINALE
keywords	CYSTEINE PROTEASE, GLYCOPROTEIN, PROLINE SPECIFICITY, CARBOHYDRATE, PAPAIN FAMILY, HYDROLASE; HYDROLASE
method	X-RAY DIFFRACTION

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	32.38 Å
rg_electron	32.20 Å
i0	165559000.00
molecular_weight	96871.0 kDa
excluded_volume	118590 Å³
envelope_volume	152250 Å³
shell_volume	40718 Å³
envelope_diameter	114.0 Å
shell_rg	38.05 Å
envelope_rg	31.56 Å
shape_rg	32.20 Å
total_rg	32.62 Å
total_atoms	6798
n_residues	864
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

▼

3. P(r) Analysis (GNOM)

dmax	108.5 Å
rg_real	32.41 Å
rg_real_error	0.77 Å
i0_real	1.6560e+08
i0_real_error	2.7440e+06
rg_reciprocal	32.40 Å
i0_reciprocal	165600000.0000
total_estimate	0.6936
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	42.1 Å
skewness	0.399
kurtosis	-0.135
angular_range	— – 0.2450 Å⁻¹
current_alpha	0.0001
highest_alpha	33000000.0000
n_real_points	50
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.810; Stabil: 1.000; Sysdev: 0.242; Positv: 1.000; Valcen: 0.993; Smooth: 0.863

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (7)

Entity 1 polymer

description	PROTEIN (PROTEASE II)
formula_weight	23941.3 kDa
src_method	nat
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	7171

DDLPDSIDWRENGAVVPVKNQGGCGSCWAFSTVAAVEGINQIVTGDLISLSEQQLVDCTTANHGCRGGWMNPAFQFIVNNGGINSEETYPYRGQDGICNSTVNAPVVSIDSYENVPSHNEQSLQKAVANQPVSVTMDAAGRDFQLYRSGIFTGSCNISANHALTVVGYGTENDKDFWIVKNSWGKNWGESGYIRAERNIENPDGKCGITRFASYPVKKGTN

Entity 2 branched

description	beta-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	570.5 kDa
src_method	man
entity_count	1

Entity 3 branched

description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	424.4 kDa
src_method	man
entity_count	1

Entity 4 branched

description	alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	570.5 kDa
src_method	man
entity_count	3

Entity 5 non-polymer

description	THIOSULFATE
formula_weight	112.1 kDa
src_method	syn
entity_count	4

Entity 6 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	man
entity_count	1

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	373

▶

6. Citations (1)

▶

length_a	93.980 Å
length_b	45.450 Å
length_c	110.040 Å
angle_alpha	90.00 °
angle_beta	105.03 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.100 Å
resolution_low	25.000 Å
r_factor	0.2130
r_work	0.2130
r_free	0.2490

fit	/app/data/saxs_computation/cq/1cqd/1cqd.fit
pddf	/app/data/pr_computation/cq/1cqd/1cqd.pr.out
profile	/app/data/saxs_computation/cq/1cqd/1cqd.dat