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1dy7

Cytochrome cd1 Nitrite Reductase, CO complex

Method: X-RAY DIFFRACTION D_max: 108.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1dy7
deposition_date	2000-01-28
title	Cytochrome cd1 Nitrite Reductase, CO complex
keywords	ENZYME, NITRITE REDUCTASE, 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	33.17 Å
rg_electron	32.68 Å
i0	189008000.00
molecular_weight	109850.0 kDa
excluded_volume	136900 Å³
envelope_volume	162660 Å³
shell_volume	41847 Å³
envelope_diameter	110.8 Å
shell_rg	39.20 Å
envelope_rg	32.86 Å
shape_rg	32.70 Å
total_rg	33.09 Å
total_atoms	7745
n_residues	970
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	108.6 Å
rg_real	33.25 Å
rg_real_error	0.78 Å
i0_real	1.8900e+08
i0_real_error	3.5550e+06
rg_reciprocal	33.22 Å
i0_reciprocal	189000000.0000
total_estimate	0.8834
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	33.9 Å
skewness	0.376
kurtosis	-0.487
angular_range	— – 0.2400 Å⁻¹
current_alpha	0.0000
highest_alpha	58380000.0000
n_real_points	49
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.880; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.962; Smooth: 0.878

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	NITRITE REDUCTASE
formula_weight	62546.5 kDa
ec_number	1.7.2.1, 1.7.99.1
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	8592

QEQVAPPKDPAAALEDHKTRTDNRYEPSLDNLAQQDVAAPGAPEGVSALSDAQYNEANKIYFERCAGCHGVLRKGATGKALTPDLTRDLGFDYLQSFITYGSPAGMPNWGTSGELSAEQVDLMANYLLLDPAAPPEFGMKEMRESWKVHVAPEDRPTQQENDWDLENLFSVTLRDAGQIALIDGATYEIKSVLDTGYAVHISRLSASGRYLFVIGRDGKVNMIDLWMKEPTTVAEIKIGSEARSIETSKMEGWEDKYAIAGAYWPPQYVIMDGETLEPKKIQSTRGMTYDEQEYHPEPRVAAILASHYRPEFIVNVKETGKILLVDYTDLDNLKTTEISAERFLHDGGLDGSHRYFITAANARNKLVVIDTKEGKLVAIEDTGGQTPHPGRGANFVHPTFGPVWATSHMGDDSVALIGTDPEGHPDNAWKILDSFPALGGGSLFIKTHPNSQYLYVDATLNPEAEISGSVAVFDIKAMTGDGSDPEFKTLPIAEWAGITEGQPRVVQGEFNKDGTEVWFSVWNGKDQESALVVVDDKTLELKHVIKDERLVTPTGKFNVYNTMTDTY

Entity 2 non-polymer

description	HEME D
formula_weight	712.5 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	CARBON MONOXIDE
formula_weight	28.0 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	3

Entity 5 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	3

Entity 6 non-polymer

description	HEME C
formula_weight	618.5 kDa
src_method	syn
entity_count	1

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	847

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6. Citations (2)

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length_a	106.940 Å
length_b	61.040 Å
length_c	100.390 Å
angle_alpha	90.00 °
angle_beta	111.77 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.600 Å
resolution_low	30.000 Å
r_factor	—
r_work	0.1780
r_free	0.1990

fit	/app/data/saxs_computation/dy/1dy7/1dy7.fit
pddf	/app/data/pr_computation/dy/1dy7/1dy7.pr.out
profile	/app/data/saxs_computation/dy/1dy7/1dy7.dat