SAXSdb — 1d4m

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1. Structure Basics

entry_id	1d4m
deposition_date	1999-10-04
title	THE CRYSTAL STRUCTURE OF COXSACKIEVIRUS A9 TO 2.9 A RESOLUTION
keywords	PICORNAVIRUS STRUCTURE, RGD, UNCOATING, VIRUS-RECEPTOR INTERACTION, WIN COMPOUND, VIRUS/VIRAL PROTEIN, Icosahedral virus, Virus; VIRUS
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	29.79 Å
rg_electron	28.86 Å
i0	143043000.00
molecular_weight	93946.0 kDa
excluded_volume	117110 Å³
envelope_volume	146160 Å³
shell_volume	41014 Å³
envelope_diameter	101.6 Å
shell_rg	37.10 Å
envelope_rg	29.54 Å
shape_rg	28.85 Å
total_rg	29.65 Å
total_atoms	6603
n_residues	835
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	93.8 Å
rg_real	29.72 Å
rg_real_error	0.53 Å
i0_real	1.4300e+08
i0_real_error	2.1830e+06
rg_reciprocal	29.75 Å
i0_reciprocal	143000000.0000
total_estimate	0.8955
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	35.4 Å
skewness	0.292
kurtosis	-0.341
angular_range	— – 0.2650 Å⁻¹
current_alpha	0.0000
highest_alpha	27760000.0000
n_real_points	54
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.917; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.890

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	PROTEIN (COXSACKIEVIRUS A9)
formula_weight	33869.0 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	1
atom_count	7051

GDVEEAIERAVVHVADTMRSGPSNSASVPALTAVETGHTSQVTPSDTMQTRHVKNYHSRSESTVENFLGRSACVYMEEYKTTDNDVNKKFVAWPINTKQMVQMRRKLEMFTYLRFDMEVTFVITSRQDPGTTLAQDMPVLTHQIMYVPPGGPIPAKVDDYAWQTSTNPSIFWTEGNAPARMSIPFISIGNAYSNFYDGWSNFDQRGSYGYNTLNNLGHIYVRHVSGSSPHPITSTIRVYFKPKHTRAWVPRPPRLCQYKKAFSVDFTPTPITDTRKDINTVTTVAQSRRRGDMSTLNTH

Entity 2 polymer

description	PROTEIN (COXSACKIEVIRUS A9)
formula_weight	28885.5 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	2

SPTVEECGYSDRVRSITLGNSTITTQECANVVVGYGRWPTYLRDDEATAEDQPTQPDVATCRFYTLDSIKWEKGSVGWWWKFPEALSDMGLFGQNMQYHYLGRAGYTIHVQCNASKFHQGCLLVVCVPEAEMGGAVVGQAFSATAMANGDKAYEFTSATQSDQTKVQTAIHNAGMGVGVGNLTIYPHQWINLRTNNSATIVMPYINSVPMDNMFRHYNFTLMVIPFVKLDYADTASTYVPITVTVAPMCAEYNGLRLAQAQ

Entity 3 polymer

description	PROTEIN (COXSACKIEVIRUS A9)
formula_weight	26335.1 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	3

GLPTMNTPGSTQFLTSDDFQSPCALPQFDVTPSMNIPGEVKNLMEIAEVDSVVPVNNVQDTTDQMEMFRIPVTINAPLQQQVFGLRLQPGLDSVFKHTLLGEILNYYAHWSGSMKLTFVFCGSAMATGKFLIAYSPPGANPPKTRKDAMLGTHIIWDIGLQSSCVLCVPWISQTHYRLVQQDEYTSAGYVTCWYQTGMIVPPGTPNSSSIMCFASACNDFSVRMLRDTPFISQDNKLQ

Entity 4 polymer

description	PROTEIN (COXSACKIEVIRUS A9)
formula_weight	7352.0 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	4

GAQVSTQKTGAHETSLSAAGNSIIHYTNINYYKDAASNSANRQDFTQDPSKFTEPVKDVMIKSLPALN

Entity 5 non-polymer

description	5-(7-(4-(4,5-DIHYDRO-2-OXAZOLYL)PHENOXY)HEPTYL)-3-METHYL ISOXAZOLE
formula_weight	342.4 kDa
src_method	syn
entity_count	2

Entity 6 non-polymer

description	MYRISTIC ACID
formula_weight	228.4 kDa
src_method	syn
entity_count	1

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	448

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6. Citations (2)

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length_a	487.300 Å
length_b	358.100 Å
length_c	305.700 Å
angle_alpha	90.00 °
angle_beta	128.10 °
angle_gamma	90.00 °
z_pdb	120

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	2.900 Å
resolution_low	20.000 Å
r_factor	0.1690
r_work	0.1690
r_free	—

fit	/app/data/saxs_computation/d4/1d4m/1d4m.fit
pddf	/app/data/pr_computation/d4/1d4m/1d4m.pr.out
profile	/app/data/saxs_computation/d4/1d4m/1d4m.dat

THE CRYSTAL STRUCTURE OF COXSACKIEVIRUS A9 TO 2.9 A RESOLUTION

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

5. Entities & Polymer Info (7)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 water

6. Citations (2)

7. Files & Curves (10)

Files (7)

Curves (3)