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1ce6

MHC CLASS I H-2DB COMPLEXED WITH A SENDAI VIRUS NUCLEOPROTEIN PEPTIDE

Method: X-RAY DIFFRACTION D_max: 75.0 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1ce6
deposition_date	1999-03-17
title	MHC CLASS I H-2DB COMPLEXED WITH A SENDAI VIRUS NUCLEOPROTEIN PEPTIDE
keywords	MHC CLASS I, ANTIGEN PRESENTATION, VIRAL PEPTIDE, COMPLEX; MHC CLASS I
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	23.83 Å
rg_electron	22.85 Å
i0	34888900.00
molecular_weight	44589.0 kDa
excluded_volume	55264 Å³
envelope_volume	66605 Å³
shell_volume	24340 Å³
envelope_diameter	77.3 Å
shell_rg	29.65 Å
envelope_rg	22.98 Å
shape_rg	22.81 Å
total_rg	23.74 Å
total_atoms	3151
n_residues	382
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	75.0 Å
rg_real	23.74 Å
rg_real_error	0.35 Å
i0_real	3.4890e+07
i0_real_error	4.3840e+05
rg_reciprocal	23.76 Å
i0_reciprocal	34890000.0000
total_estimate	0.9096
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	29.3 Å
skewness	0.211
kurtosis	-0.511
angular_range	— – 0.3350 Å⁻¹
current_alpha	0.0000
highest_alpha	9119000.0000
n_real_points	65
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.942; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.996

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	PROTEIN (MHC CLASS I H-2DB HEAVY CHAIN)
formula_weight	31861.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3176

GPHSMRYFETAVSRPGLEEPRYISVGYVDNKEFVRFDSDAENPRYEPRAPWMEQEGPEYWERETQKAKGQEQWFRVSLRNLLGYYNQSAGGSHTLQQMSGCDLGSDWRLLRGYLQFAYEGRDYIALNEDLKTWTAADMAAQITRRKWEQSGAAEHYKAYLEGECVEWLHRYLKNGNATLLRTDSPKAHVTHHPRSKGEVTLRCWALGFYPADITLTWQLNGEELTQDMELVETRPAGDGTFQKWASVVVPLGKEQNYTCRVYHEGLPEPLTLRW

Source

organism	Mus musculus
common_name	house mouse
ncbi_taxonomy_id	10090
host_organism	Cricetulus griseus

Entity 2 polymer

description	PROTEIN (HUMAN BETA-2 MICROGLOBULIN)
formula_weight	12855.4 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

GPHSMRYFEIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Cricetulus griseus

Entity 3 polymer

description	PROTEIN (SENDAI VIRUS NUCLEOPROTEIN)
formula_weight	949.1 kDa
src_method	syn
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

FAPGNYPAL

Entity 4 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	25

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6. Citations (1)

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length_a	60.787 Å
length_b	58.082 Å
length_c	74.666 Å
angle_alpha	90.00 °
angle_beta	108.26 °
angle_gamma	90.00 °
z_pdb	2

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.900 Å
resolution_low	10.000 Å
r_factor	—
r_work	0.2170
r_free	0.2740

fit	/app/data/saxs_computation/ce/1ce6/1ce6.fit
pddf	/app/data/pr_computation/ce/1ce6/1ce6.pr.out
profile	/app/data/saxs_computation/ce/1ce6/1ce6.dat

MHC CLASS I H-2DB COMPLEXED WITH A SENDAI VIRUS NUCLEOPROTEIN PEPTIDE

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 (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Entity 4 non-polymer

Entity 5 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)