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1d7d

CYTOCHROME DOMAIN OF CELLOBIOSE DEHYDROGENASE, HP3 FRAGMENT, PH 7.5

Method: X-RAY DIFFRACTION D_max: 73.3 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1d7d
deposition_date	1999-10-16
title	CYTOCHROME DOMAIN OF CELLOBIOSE DEHYDROGENASE, HP3 FRAGMENT, PH 7.5
keywords	B-TYPE CYTOCHROME, MET/HIS LIGATION, BETA SANDWICH, FE(II)-PROTOPORPHYRIN IX, OXIDOREDUCTASE; OXIDOREDUCTASE
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	24.01 Å
rg_electron	22.86 Å
i0	32957400.00
molecular_weight	43291.0 kDa
excluded_volume	53281 Å³
envelope_volume	61873 Å³
shell_volume	22793 Å³
envelope_diameter	76.7 Å
shell_rg	29.29 Å
envelope_rg	22.97 Å
shape_rg	22.80 Å
total_rg	23.77 Å
total_atoms	3023
n_residues	370
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	73.3 Å
rg_real	23.99 Å
rg_real_error	0.40 Å
i0_real	3.2960e+07
i0_real_error	3.8260e+05
rg_reciprocal	23.99 Å
i0_reciprocal	32960000.0000
total_estimate	0.9087
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	25.2 Å
skewness	0.285
kurtosis	-0.593
angular_range	— – 0.3300 Å⁻¹
current_alpha	0.0000
highest_alpha	5800000.0000
n_real_points	65
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.941; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.996

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	CELLOBIOSE DEHYDROGENASE
formula_weight	20012.8 kDa
ec_number	1.1.3.25
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	3292

QSASQFTDPTTGFQFTGITDPVHDVTYGFVFPPLATSGAQSTEFIGEVVAPIASKWIGIALGGAMNNDLLLVAWANGNQIVSSTRWATGYVQPTAYTGTATLTTLPETTINSTHWKWVFRCQGCTEWNNGGGIDVTSQGVLAWAFSNVAVDDPSDPQSTFSEHTDFGFFGIDYSTAHSANYQNYLN

Entity 2 branched

description	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	586.5 kDa
src_method	man
entity_count	1

Entity 3 branched

description	alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	586.5 kDa
src_method	man
entity_count	1

Entity 4 non-polymer

description	CADMIUM ION
formula_weight	112.4 kDa
src_method	syn
entity_count	6

Entity 5 non-polymer

description	PROTOPORPHYRIN IX CONTAINING FE
formula_weight	616.5 kDa
src_method	syn
entity_count	2

Entity 6 non-polymer

description	2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
formula_weight	252.3 kDa
src_method	syn
entity_count	1

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	269

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6. Citations (1)

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length_a	138.300 Å
length_b	138.300 Å
length_c	53.390 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	12

space_group	P 65
int_tables_number	170
crystal_system	—

resolution	1.900 Å
resolution_low	25.000 Å
r_factor	0.1870
r_work	0.1870
r_free	0.2210

fit	/app/data/saxs_computation/d7/1d7d/1d7d.fit
pddf	/app/data/pr_computation/d7/1d7d/1d7d.pr.out
profile	/app/data/saxs_computation/d7/1d7d/1d7d.dat