SAXSdb — 1aym

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1. Structure Basics

entry_id	1aym
deposition_date	1997-11-06
title	HUMAN RHINOVIRUS 16 COAT PROTEIN AT HIGH RESOLUTION
keywords	HUMAN RHINOVIRUS 16, RNA, SITE-DIRECTED MUTAGENESIS, RHINOVIRUS COAT 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	29.60 Å
rg_electron	28.73 Å
i0	130907000.00
molecular_weight	90411.0 kDa
excluded_volume	112980 Å³
envelope_volume	140480 Å³
shell_volume	39721 Å³
envelope_diameter	101.5 Å
shell_rg	36.77 Å
envelope_rg	29.38 Å
shape_rg	28.71 Å
total_rg	29.53 Å
total_atoms	6363
n_residues	804
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	96.9 Å
rg_real	29.53 Å
rg_real_error	0.60 Å
i0_real	1.3090e+08
i0_real_error	2.1280e+06
rg_reciprocal	29.56 Å
i0_reciprocal	130900000.0000
total_estimate	0.8914
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	35.9 Å
skewness	0.291
kurtosis	-0.335
angular_range	— – 0.2700 Å⁻¹
current_alpha	0.0000
highest_alpha	28010000.0000
n_real_points	55
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.871; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.973

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	HUMAN RHINOVIRUS 16 COAT PROTEIN
formula_weight	32501.4 kDa
mutation	N-TERMINAL MYRISTOYLATION ON VP4
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	1
atom_count	6975

NPVERYVDEVLNEVLVVPNINQSHPTTSNAAPVLDAAETGHTNKIQPEDTIETRYVQSSQTLDEMSVESFLGRSGCIHESVLDIVDNYNDQSFTKWNINLQEMAQIRRKFEMFTYARFDSEITMVPSVAAKDGHIGHIVMQYMYVPPGAPIPTTRDDYAWQSGTNASVFWQHGQPFPRFSLPFLSIASAYYMFYDGYDGDTYKSRYGTVVTNDMGTLCSRIVTSEQLHKVKVVTRIYHKAKHTKAWCPRPPRAVQYSHTHTTNYKLSSEVHNDVAIRPRTNLTTV

Source

organism	Human rhinovirus sp.
ncbi_taxonomy_id	169066
host_organism	Homo sapiens

Entity 2 polymer

description	HUMAN RHINOVIRUS 16 COAT PROTEIN
formula_weight	28990.6 kDa
mutation	N-TERMINAL MYRISTOYLATION ON VP4
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	2

SPSVEACGYSDRIIQITRGDSTITSQDVANAVVGYGVWPHYLTPQDATAIDKPTQPDTSSNRFYTLDSKMWNSTSKGWWWKLPDALKDMGIFGENMFYHFLGRSGYTVHVQCNASKFHQGTLLVVMIPEHQLATVNKGNVNAGYKYTHPGEAGREVGTQVENEKQPSDDNWLNFDGTLLGNLLIFPHQFINLRSNNSATLIVPYVNAVPMDSMVRHNNWSLVIIPVCQLQSNNISNIVPITVSISPMCAEFSGARAKTVVQ

Source

organism	Human rhinovirus sp.
ncbi_taxonomy_id	169066
host_organism	Homo sapiens

Entity 3 polymer

description	HUMAN RHINOVIRUS 16 COAT PROTEIN
formula_weight	26314.2 kDa
mutation	N-TERMINAL MYRISTOYLATION ON VP4
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	3

GLPVYVTPGSGQFMTTDDMQSPCALPWYHPTKEIFIPGEVKNLIEMCQVDTLIPINSTQSNIGNVSMYTVTLSPQTKLAEEIFAIKVDIASHPLATTLIGEIASYFTHWTGSLRFSFMFCGTANTTLKVLLAYTPPGIGKPRSRKEAMLGTHVVWDVGLQSTVSLVVPWISASQYRFTTPDTYSSAGYITCWYQTNFVVPPNTPNTAEMLCFVSGCKDFCLRMARDTDLHKQTGPITQ

Source

organism	Human rhinovirus sp.
ncbi_taxonomy_id	169066
host_organism	Homo sapiens

Entity 4 polymer

description	HUMAN RHINOVIRUS 16 COAT PROTEIN
formula_weight	7374.0 kDa
mutation	N-TERMINAL MYRISTOYLATION ON VP4
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	4

GAQVSRQNVGTHSTQNMVSNGSSLNYFNINYFKDAASSGASRLDFSQDPSKFTDPVKDVLEKGIPTLQ

Source

organism	Human rhinovirus sp.
ncbi_taxonomy_id	169066
host_organism	Homo sapiens

Entity 5 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	1

Entity 6 non-polymer

description	LAURIC ACID
formula_weight	200.3 kDa
src_method	syn
entity_count	1

Entity 7 non-polymer

description	MYRISTIC ACID
formula_weight	228.4 kDa
src_method	syn
entity_count	1

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	533

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6. Citations (8)

The refined structure of human rhinovirus 16 at 2.15 A resolution: implications for the viral life cycle.

Structure (1997)

PMID: 9083115 · DOI: 10.1016/S0969-2126(97)00199-8 PRIMARY

The Structure of Human Rhinovirus 16

Structure (1993)

A Comparison of the Anti-Rhinoviral Drug Binding Pocket in Hrv14 and Hrv1A

J.Mol.Biol. (1993)

Structure of a Human Rhinovirus Complexed with its Receptor Molecule

Proc.Natl.Acad.Sci.USA (1993)

Crystal Structure of Human Rhinovirus Serotype 1A (Hrv1A)

J.Mol.Biol. (1989)

Common Cold Viruses

Trends Biochem.Sci. (1987)

The Site of Attachment in Human Rhinovirus 14 for Antiviral Agents that Inhibit Uncoating

Science (1986)

Structure of a Human Common Cold Virus and Functional Relationship to Other Picornaviruses

Nature (1985)

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length_a	362.600 Å
length_b	347.100 Å
length_c	334.900 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	120

space_group	P 2 21 21
int_tables_number	18
crystal_system	—

resolution	2.150 Å
resolution_low	8.000 Å
r_factor	0.2300
r_work	0.2300
r_free	0.2330

fit	/app/data/saxs_computation/ay/1aym/1aym.fit
pddf	/app/data/pr_computation/ay/1aym/1aym.pr.out
profile	/app/data/saxs_computation/ay/1aym/1aym.dat

HUMAN RHINOVIRUS 16 COAT PROTEIN AT HIGH 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

Diffraction

5. Entities & Polymer Info (8)

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 water

6. Citations (8)

7. Files & Curves (10)

Files (7)

Curves (3)