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1dbo

CRYSTAL STRUCTURE OF CHONDROITINASE B

Method: X-RAY DIFFRACTION D_max: 77.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1dbo
deposition_date	1999-11-03
title	CRYSTAL STRUCTURE OF CHONDROITINASE B
keywords	ACTIVE SITE, BETA-ELIMINATION, DEMATAN SULFATE, LYASE; LYASE
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	23.45 Å
rg_electron	22.76 Å
i0	50794600.00
molecular_weight	55272.0 kDa
excluded_volume	69084 Å³
envelope_volume	78888 Å³
shell_volume	28298 Å³
envelope_diameter	80.2 Å
shell_rg	30.56 Å
envelope_rg	23.15 Å
shape_rg	22.71 Å
total_rg	23.81 Å
total_atoms	3885
n_residues	480
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	77.9 Å
rg_real	23.39 Å
rg_real_error	0.40 Å
i0_real	5.0790e+07
i0_real_error	7.1810e+05
rg_reciprocal	23.41 Å
i0_reciprocal	50800000.0000
total_estimate	0.8765
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	27.6 Å
skewness	0.348
kurtosis	-0.199
angular_range	— – 0.3400 Å⁻¹
current_alpha	0.0001
highest_alpha	12150000.0000
n_real_points	66
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.798; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.994

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	CHONDROITINASE B
formula_weight	56392.3 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	4365

MKMLNKLAGYLLPIMVLLNVAPCLGQVVASNETLYQVVKEVKPGGLVQIADGTYKDVQLIVSNSGKSGLPITIKALNPGKVFFTGDAKVELRGEHLILEGIWFKDGNRAIQAWKSHGPGLVAIYGSYNRITACVFDCFDEANSAYITTSLTEDGKVPQHCRIDHCSFTDKITFDQVINLNNTARAIKDGSVGGPGMYHRVDHCFFSNPQKPGNAGGGIRIGYYRNDIGRCLVDSNLFMRQDSEAEIITSKSQENVYYGNTYLNCQGTMNFRHGDHQVAINNFYIGNDQRFGYGGMFVWGSRHVIACNYFELSETIKSRGNAALYLNPGAMASEHALAFDMLIANNAFINVNGYAIHFNPLDERRKEYCAANRLKFETPHQLMLKGNLFFKDKPYVYPFFKDDYFIAGKNSWTGNVALGVEKGIPVNISANRSAYKPVKIKDIQPIEGIALDLNALISKGITGKPLSWDEVRPYWLKEMPGTYALTARLSADRAAKFKAVIKRNKEH

Entity 2 branched

description	;4-deoxy-alpha-D-glucopyranose-(1-3)-[beta-D-glucopyranose-(1-4)]2-O-methyl-beta-L-fucopyranose-(1-4)-beta-D-xylopyranose-(1-4)-alpha-D-glucopyranuronic acid-(1-2)-[alpha-L-rhamnopyranose-(1-4)]alpha-D-mannopyranose ;
formula_weight	1103.0 kDa
src_method	man
entity_count	1

Entity 3 branched

description	4-deoxy-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose
formula_weight	461.4 kDa
src_method	man
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	475

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6. Citations (1)

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length_a	50.600 Å
length_b	74.400 Å
length_c	58.700 Å
angle_alpha	90.00 °
angle_beta	92.90 °
angle_gamma	90.00 °
z_pdb	2

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.700 Å
resolution_low	19.950 Å
r_factor	0.1780
r_work	0.1810
r_free	0.2170

fit	/app/data/saxs_computation/db/1dbo/1dbo.fit
pddf	/app/data/pr_computation/db/1dbo/1dbo.pr.out
profile	/app/data/saxs_computation/db/1dbo/1dbo.dat

CRYSTAL STRUCTURE OF CHONDROITINASE B

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