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12qj

Pneumococcal choline binding CbpE surface protein bounds to 5992-2 Fab

Method: ELECTRON MICROSCOPY D_max: 103.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	12qj
deposition_date	2026-04-15
title	Pneumococcal choline binding CbpE surface protein bounds to 5992-2 Fab
keywords	PNEUMOCOCCAL CHOLINE BINDING, CryoEM, HUMAN MONOCLONAL ANTIBODY, IMMUNE SYSTEM; IMMUNE SYSTEM
method	ELECTRON MICROSCOPY

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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	31.40 Å
rg_electron	31.24 Å
i0	81498700.00
molecular_weight	70472.0 kDa
excluded_volume	87609 Å³
envelope_volume	108310 Å³
shell_volume	30056 Å³
envelope_diameter	108.0 Å
shell_rg	36.64 Å
envelope_rg	31.30 Å
shape_rg	31.16 Å
total_rg	31.95 Å
total_atoms	4987
n_residues	630
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	103.7 Å
rg_real	31.61 Å
rg_real_error	1.22 Å
i0_real	8.1500e+07
i0_real_error	1.2660e+06
rg_reciprocal	31.53 Å
i0_reciprocal	81490000.0000
total_estimate	0.8609
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	29.0 Å
skewness	0.424
kurtosis	-0.562
angular_range	— – 0.2500 Å⁻¹
current_alpha	0.0000
highest_alpha	11720000.0000
n_real_points	51
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.823; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.876; Smooth: 0.843

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Choline binding protein E CbpE
formula_weight	45515.3 kDa
ec_number	3.2.1.96
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	4987

SSGNKIHFINVQEGGSDAIILESNGHFAMVDTGEDYDFPDGSDSRYPWREGIETSYKHVLTDRVFRRLKELGVQKLDFILVTHTHSDHIGNVDELLSTYPVDRVYLKKYSDNRITNSERLWDNLYGYDKVLQTASEKGVSVIQNITQGDAHFQFGDMDIQLYNYENETDSSGELKKIWDDNSNSLISVVKVNGKKIYLGGDLDNVHGAEDKYGPLIGKVDLMKFNHHHDTNKSNTKDFIKNLSPSLIVQTSDSLPWKNGVDSEYVNWLKERGIERINAASKDYDATVFDIRQDGLVNISTSYKPIPSFQAGWHKSSYGNWWYQAPDSTGEYAVGWNEIKGEWYYFNQTGILLQNQWKKWNNRWFYLTDSGVAAKNWKKIAGIWYYFNKENQMEI

Source

organism	Streptococcus pneumoniae
ncbi_taxonomy_id	1313
host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 polymer

description	5992-2 Fab Heavy Chain
formula_weight	13679.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

QVQLQESGPRLVKVSETLSLTCSLSGHSISSGHHWAWIRQSPGRGLEWIATVDHNGRTYYNPSLRGRVILSKDTTKNSFSVQLTSVTAADTAVYYCARREAPSPGTGWYPPFGQWGQGALVTVST

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 3 polymer

description	5992-2 Fab Light Chain
formula_weight	11381.6 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

QSVLTQPPSLSGAPGQTVTISCTGSSSNIGAGYDVHWYRQLPGTAPTLLISVFDNRPLGVPGRISGSKSGTSASLAITGLQAEDEADYYCQSHDNMLSGSVFGGGTKLTVL

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	3.350 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.35 Å
resolution_method	—
num_particles	59000

fit	/app/data/saxs_computation/2q/12qj/12qj.fit
pddf	/app/data/pr_computation/2q/12qj/12qj.pr.out
profile	/app/data/saxs_computation/2q/12qj/12qj.dat

Pneumococcal choline binding CbpE surface protein bounds to 5992-2 Fab

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

EM 3D

5. Entities & Polymer Info (3)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)