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1ar1

;Structure at 2.7 Angstrom Resolution of the Paracoccus Denitrificans two-subunit Cytochrome C Oxidase Complexed with an Antibody Fv Fragment ;

Method: X-RAY DIFFRACTION D_max: 115.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1ar1
deposition_date	1997-08-08
title	;Structure at 2.7 Angstrom Resolution of the Paracoccus Denitrificans two-subunit Cytochrome C Oxidase Complexed with an Antibody Fv Fragment ;
keywords	;COMPLEX (OXIDOREDUCTASE-ANTIBODY), ELECTRON TRANSPORT, TRANSMEMBRANE, CYTOCHROME OXIDASE, ANTIBODY COMPLEX, COMPLEX (OXIDOREDUCTASE-ANTIBODY) complex ;; COMPLEX (OXIDOREDUCTASE/ANTIBODY)
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	33.85 Å
rg_electron	33.13 Å
i0	174128000.00
molecular_weight	116060.0 kDa
excluded_volume	148940 Å³
envelope_volume	170100 Å³
shell_volume	43595 Å³
envelope_diameter	123.7 Å
shell_rg	39.21 Å
envelope_rg	33.61 Å
shape_rg	33.12 Å
total_rg	33.64 Å
total_atoms	8191
n_residues	1007
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	115.0 Å
rg_real	34.00 Å
rg_real_error	0.99 Å
i0_real	1.7410e+08
i0_real_error	3.1070e+06
rg_reciprocal	33.91 Å
i0_reciprocal	174100000.0000
total_estimate	0.8568
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	34.3 Å
skewness	0.490
kurtosis	-0.314
angular_range	— – 0.2350 Å⁻¹
current_alpha	0.0000
highest_alpha	40550000.0000
n_real_points	48
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.796; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.855; Smooth: 0.890

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4. Crystallography & Experiment

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5. Entities & Polymer Info (10)

Entity 1 polymer

description	CYTOCHROME C OXIDASE
formula_weight	62486.6 kDa
ec_number	1.9.3.1
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	8243

MADAAVHGHGDHHDTRGFFTRWFMSTNHKDIGILYLFTAGIVGLISVCFTVYMRMELQHPGVQYMCLEGARLIADASAECTPNGHLWNVMITYHGVLMMFFVVIPALFGGFGNYFMPLHIGAPDMAFPRLNNLSYWMYVCGVALGVASLLAPGGNDQMGSGVGWVLYPPLSTTEAGYSMDLAIFAVHVSGASSILGAINIITTFLNMRAPGMTLFKVPLFAWSVFITAWLILLSLPVLAGAITMLLMDRNFGTQFFDPAGGGDPVLYQHILWFFGHPEVYIIILPGFGIISHVISTFAKKPIFGYLPMVLAMAAIGILGFVVWAHHMYTAGMSLTQQAYFMLATMTIAVPTGIKVFSWIATMWGGSIEFKTPMLWAFGFLFLFTVGGVTGVVLSQAPLDRVYHDTYYVVAHFHYVMSLGAVFGIFAGVYYWIGKMSGRQYPEWAGQLHFWMMFIGSNLIFFPQHFLGRQGMPRRYIDYPVEFAYWNNISSIGAYISFASFLFFIGIVFYTLFAGKRVNVPNYWNEHADTLEWTLPSPPPEHTFETLPKREDWDRAHAH

Source

organism	Paracoccus denitrificans
ncbi_taxonomy_id	266
host_organism	Escherichia coli

Entity 2 polymer

description	CYTOCHROME C OXIDASE
formula_weight	32563.6 kDa
ec_number	1.9.3.1
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MMAIATKRRGVAAVMSLGVATMTAVPALAQDVLGDLPVIGKPVNGGMNFQPASSPLAHDQQWLDHFVLYIITAVTIFVCLLLLICIVRFNRRANPVPARFTHNTPIEVIWTLVPVLILVAIGAFSLPILFRSQEMPNDPDLVIKAIGHQWYWSYEYPNDGVAFDALMLEKEALADAGYSEDEYLLATDNPVVVPVGKKVLVQVTATDVIHAWTIPAFAVKQDAVPGRIAQLWFSVDQEGVYFGQCSELCGINHAYMPIVVKAVSQEKYEAWLAGAKEEFAADASDYLPASPVKLASAE

Source

organism	Paracoccus denitrificans
ncbi_taxonomy_id	266
host_organism	Escherichia coli

Entity 3 polymer

description	ANTIBODY FV FRAGMENT
formula_weight	14324.9 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

EVKLQESGGDLVQPGGSLKLSCAASGFTFSSYTMSWVRQTPEKRLEWVASINNGGGRTYYPDTVKGRFTISRDNAKNTLYLQMSSLKSEDTAMYYCVRHEYYYAMDYWGQGTTVTVSSAWRHPQFGG

Source

organism	Mus musculus
common_name	house mouse
ncbi_taxonomy_id	10090
host_organism	Escherichia coli

Entity 4 polymer

description	ANTIBODY FV FRAGMENT
formula_weight	13260.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	D

DIELTQTPVSLSASVGETVTITCRASENIYSYLAWYQQKQGKSPQFLVYNAKTLGEGVPSRFSGSGSGTQFSLKINSLLPEDFGSYYCQHHYGTPPLTFGGGTKLEIKREQKLISEEDLM

Source

organism	Mus musculus
common_name	house mouse
ncbi_taxonomy_id	10090
host_organism	Escherichia coli

Entity 5 non-polymer

description	COPPER (II) ION
formula_weight	63.5 kDa
src_method	syn
entity_count	3

Entity 6 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	1

Entity 7 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	1

Entity 8 non-polymer

description	HEME-A
formula_weight	852.8 kDa
src_method	syn
entity_count	2

Entity 9 non-polymer

description	LAURYL DIMETHYLAMINE-N-OXIDE
formula_weight	229.4 kDa
src_method	syn
entity_count	9

Entity 10 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	52

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6. Citations (1)

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length_a	93.500 Å
length_b	151.000 Å
length_c	156.700 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	2.700 Å
resolution_low	30.000 Å
r_factor	0.2070
r_work	0.2070
r_free	0.2610

fit	/app/data/saxs_computation/ar/1ar1/1ar1.fit
pddf	/app/data/pr_computation/ar/1ar1/1ar1.pr.out
profile	/app/data/saxs_computation/ar/1ar1/1ar1.dat

;Structure at 2.7 Angstrom Resolution of the Paracoccus Denitrificans two-subunit Cytochrome C Oxidase Complexed with an Antibody Fv Fragment ;

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 (10)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 non-polymer

Entity 9 non-polymer

Entity 10 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)