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1ddh

;MHC CLASS I H-2DD HEAVY CHAIN COMPLEXED WITH BETA-2 MICROGLOBULIN AND AN IMMUNODOMINANT PEPTIDE P18-I10 FROM THE HUMAN IMMUNODEFICIENCY VIRUS ENVELOPE GLYCOPROTEIN 120 ;

Method: X-RAY DIFFRACTION D_max: 72.0 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1ddh
deposition_date	1998-06-22
title	;MHC CLASS I H-2DD HEAVY CHAIN COMPLEXED WITH BETA-2 MICROGLOBULIN AND AN IMMUNODOMINANT PEPTIDE P18-I10 FROM THE HUMAN IMMUNODEFICIENCY VIRUS ENVELOPE GLYCOPROTEIN 120 ;
keywords	;COMPLEX (HISTOCOMPATIBILITY-ANTIGEN), HISTOCOMPATIBILITY ANTIGEN, CLASS I MAJOR HISTOCOMPATIBILITY COMPLEX, MHC I, COMPLEX (HISTOCOMPATIBILITY-ANTIGEN) complex ;; COMPLEX (HISTOCOMPATIBILITY/ANTIGEN)
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	23.45 Å
rg_electron	22.37 Å
i0	34685900.00
molecular_weight	43191.0 kDa
excluded_volume	53011 Å³
envelope_volume	65044 Å³
shell_volume	24279 Å³
envelope_diameter	73.7 Å
shell_rg	29.11 Å
envelope_rg	22.40 Å
shape_rg	22.36 Å
total_rg	23.19 Å
total_atoms	3047
n_residues	383
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	72.0 Å
rg_real	23.36 Å
rg_real_error	0.40 Å
i0_real	3.4690e+07
i0_real_error	4.9450e+05
rg_reciprocal	23.38 Å
i0_reciprocal	34690000.0000
total_estimate	0.9130
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	29.9 Å
skewness	0.191
kurtosis	-0.504
angular_range	— – 0.3400 Å⁻¹
current_alpha	0.0000
highest_alpha	8287000.0000
n_real_points	66
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.957; 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 (4)

Entity 1 polymer

description	MHC CLASS I H-2DD HEAVY CHAIN
formula_weight	31862.4 kDa
mutation	G1M
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3051

MSHSLRYFVTAVSRPGFGEPRYMEVGYVDNTEFVRFDSDAENPRYEPRARWIEQEGPEYWERETRRANGNEQSFRVDLRTALRYYNQSAGGSHTLQWMAGCDVESDGRLLRGYWQFAYDGCDYIALNEDLKTWTAADMAAQITRRKWEQAGAAERDRAYLEGECVEWLRRYLKNGNATLLATDPPKAHVTHHRRPEGDVTLRCWALGFYPAEITLTWQLNGEELTQEMELVETRPAGDGTFQKWASVVVPLGKQQKYTCHVEHEGLPEPLTLRW

Source

organism	Mus musculus
common_name	house mouse
ncbi_taxonomy_id	10090
host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

description	BETA-2 MICROGLOBULIN
formula_weight	11678.4 kDa
mutation	I1M
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDWSFYILAHTEFTPTETDTYACRVKHASMAEPKTVYWDRDM

Source

organism	Mus musculus
common_name	house mouse
ncbi_taxonomy_id	10090
host_organism	Escherichia coli BL21(DE3)

Entity 3 polymer

description	HUMAN IMMUNODEFICIENCY VIRUS ENVELOPE GLYCOPROTEIN 120
formula_weight	1075.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	P

RGPGRAFVTI

Source

organism	Human immunodeficiency virus 1
ncbi_taxonomy_id	11676

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	4

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6. Citations (2)

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length_a	51.330 Å
length_b	91.350 Å
length_c	108.200 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	3.100 Å
resolution_low	8.000 Å
r_factor	0.2290
r_work	0.2290
r_free	0.3370

fit	/app/data/saxs_computation/dd/1ddh/1ddh.fit
pddf	/app/data/pr_computation/dd/1ddh/1ddh.pr.out
profile	/app/data/saxs_computation/dd/1ddh/1ddh.dat

;MHC CLASS I H-2DD HEAVY CHAIN COMPLEXED WITH BETA-2 MICROGLOBULIN AND AN IMMUNODOMINANT PEPTIDE P18-I10 FROM THE HUMAN IMMUNODEFICIENCY VIRUS ENVELOPE GLYCOPROTEIN 120 ;

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 (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 water

6. Citations (2)

7. Files & Curves (10)

Files (7)

Curves (3)