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1diy

CRYSTAL STRUCTURE OF ARACHIDONIC ACID BOUND IN THE CYCLOOXYGENASE ACTIVE SITE OF PGHS-1

Method: X-RAY DIFFRACTION D_max: 78.5 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1diy
deposition_date	1999-11-30
title	CRYSTAL STRUCTURE OF ARACHIDONIC ACID BOUND IN THE CYCLOOXYGENASE ACTIVE SITE OF PGHS-1
keywords	ARACHIDONIC ACID, MEMBRANE PROTEIN, PEROXIDASE, DIOXYGENASE, 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	25.30 Å
rg_electron	24.13 Å
i0	65895900.00
molecular_weight	66232.0 kDa
excluded_volume	83907 Å³
envelope_volume	97375 Å³
shell_volume	32523 Å³
envelope_diameter	79.8 Å
shell_rg	32.32 Å
envelope_rg	24.45 Å
shape_rg	24.10 Å
total_rg	25.12 Å
total_atoms	4671
n_residues	553
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	78.5 Å
rg_real	25.18 Å
rg_real_error	0.42 Å
i0_real	6.5900e+07
i0_real_error	8.8140e+05
rg_reciprocal	25.22 Å
i0_reciprocal	65900000.0000
total_estimate	0.9023
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	32.4 Å
skewness	0.186
kurtosis	-0.413
angular_range	— – 0.3150 Å⁻¹
current_alpha	0.0000
highest_alpha	9979000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.917; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.982

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	PROSTAGLANDIN H2 SYNTHASE-1
formula_weight	63724.1 kDa
ec_number	1.14.99.1
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	4780

PVNPCCYYPCQHQGICVRFGLDRYQCDCTRTGYSGPNCTIPEIWTWLRTTLRPSPSFIHFLLTHGRWLWDFVNATFIRDTLMRLVLTVRSNLIPSPPTYNIAHDYISWESFSNVSYYTRILPSVPRDCPTPMGTKGKKQLPDAEFLSRRFLLRRKFIPDPQGTNLMFAFFAQHFTHQFFKTSGKMGPGFTKALGHGVDLGHIYGDNLERQYQLRLFKDGKLKYQMLNGEVYPPSVEEAPVLMHYPRGIPPQSQMAVGQEVFGLLPGLMLYATIWLREHNRVCDLLKAEHPTWGDEQLFQTARLILIGETIKIVIEEYVQQLSGYFLQLKFDPELLFGAQFQYRNRIAMEFNQLYHWHPLMPDSFRVGPQDYSYEQFLFNTSMLVDYGVEALVDAFSRQPAGRIGGGRNIDHHILHVAVDVIKESRVLRLQPFNEYRKRFGMKPYTSFQELTGEKEMAAELEELYGDIDALEFYPGLLLEKCHPNSIFGESMIEMGAPFSLKGLLGNPICSPEYWKASTFGGEVGFNLVKTATLKKLVCLNTKTCPYVSFHVPD

Entity 2 branched

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

Entity 3 branched

description	;alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
formula_weight	910.8 kDa
src_method	man
entity_count	1

Entity 4 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 5 non-polymer

description	octyl beta-D-glucopyranoside
formula_weight	292.4 kDa
src_method	syn
entity_count	4

Entity 6 non-polymer

description	PROTOPORPHYRIN IX CONTAINING CO
formula_weight	619.6 kDa
src_method	syn
entity_count	1

Entity 7 non-polymer

description	ARACHIDONIC ACID
formula_weight	304.5 kDa
src_method	syn
entity_count	1

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	109

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6. Citations (1)

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length_a	182.100 Å
length_b	182.100 Å
length_c	103.640 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	12

space_group	P 65 2 2
int_tables_number	179
crystal_system	—

resolution	3.000 Å
resolution_low	9.000 Å
r_factor	0.2160
r_work	0.2150
r_free	0.2900

fit	/app/data/saxs_computation/di/1diy/1diy.fit
pddf	/app/data/pr_computation/di/1diy/1diy.pr.out
profile	/app/data/saxs_computation/di/1diy/1diy.dat