← Back to search

9rm2

BKPyV VP1 IN COMPLEX WITH 319C07-FAB

Method: X-RAY DIFFRACTION D_max: 159.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9rm2
deposition_date	2025-06-17
title	BKPyV VP1 IN COMPLEX WITH 319C07-FAB
keywords	FAB ANTIBODY BKPyV VP1 virus capsid, VIRAL PROTEIN; VIRAL PROTEIN
method	X-RAY DIFFRACTION

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	50.20 Å
rg_electron	49.94 Å
i0	2197810000.00
molecular_weight	390090.0 kDa
excluded_volume	487240 Å³
envelope_volume	680510 Å³
shell_volume	108360 Å³
envelope_diameter	162.3 Å
shell_rg	57.53 Å
envelope_rg	49.68 Å
shape_rg	49.89 Å
total_rg	50.37 Å
total_atoms	27450
n_residues	3522
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

▼

3. P(r) Analysis (GNOM)

dmax	159.6 Å
rg_real	50.00 Å
rg_real_error	0.91 Å
i0_real	2.1980e+09
i0_real_error	3.5220e+07
rg_reciprocal	50.35 Å
i0_reciprocal	2199000000.0000
total_estimate	0.8909
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	66.9 Å
skewness	0.124
kurtosis	-0.508
angular_range	— – 0.1550 Å⁻¹
current_alpha	0.0001
highest_alpha	183200000.0000
n_real_points	32
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.908; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.978; Smooth: 0.875

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (12)

Entity 1 polymer

description	319C07 antibody heavy chain, Fab fragment
formula_weight	24208.1 kDa
src_method	man
entity_count	5

Polymer

type	polypeptide(L)
strand_id	H,A,D,G,M
atom_count	29832

QVQLQQWGAGLLKPSETLSLTCAVYRGSFSAYYWTWFRQPPGKGLEWIGEINHRGYTNYNPSLRGRVSISVDTSKKQFSLKLRSVNAADTAVYYCATLRSTSGWHDYFDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Cricetulus griseus

Entity 2 polymer

description	319C07 antibody light chain, Fab fragment
formula_weight	23297.9 kDa
src_method	man
entity_count	5

Polymer

type	polypeptide(L)
strand_id	L,B,E,J,N

EIVLTQSPGTLSLSPGERATLSCRASQSVSSSYLAWYQQTPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFVVYFCLQYGSSPLTFGPGTKVDIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Cricetulus griseus

Entity 3 polymer

description	Major capsid protein VP1
formula_weight	32965.4 kDa
mutation	C105S
src_method	man
entity_count	5

Polymer

type	polypeptide(L)
strand_id	P,C,F,K,O

MAPTKRKGECPGAAPKKPKEPVQVPKLLIKGGVEVLEVKTGVDAITEVECFLNPEMGDPDENLRGFSLKLSAENDFSSDSPERKMLPCYSTARIPLPNLNEDLTSGNLLMWEAVTVQTEVIGITSMLNLHAGSQKVHEHGGGKPIQGSNFHFFAVGGDPLEMQGVLMNYRTKYPDGTITPKNPTAQSQVMNTDHKAYLDKNNAYPVECWVPDPSRNENTRYFGTFTGGENVPPVLHVTNTATTVLLDEQGVGPLCKADSLYVSAADICGLFTNSSGTQQWRGLARYFKIRLRKRSVKNPY

Source

organism	Betapolyomavirus hominis
ncbi_taxonomy_id	1891762
host_organism	Escherichia coli

Entity 4 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	9

Entity 5 non-polymer

description	TRIETHYLENE GLYCOL
formula_weight	150.2 kDa
src_method	syn
entity_count	9

Entity 6 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	23

Entity 7 non-polymer

description	TETRAETHYLENE GLYCOL
formula_weight	194.2 kDa
src_method	syn
entity_count	6

Entity 8 non-polymer

description	1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE
formula_weight	178.2 kDa
src_method	syn
entity_count	2

Entity 9 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	syn
entity_count	9

Entity 10 non-polymer

description	PENTAETHYLENE GLYCOL
formula_weight	238.3 kDa
src_method	syn
entity_count	1

Entity 11 non-polymer

description	HEXAETHYLENE GLYCOL
formula_weight	282.3 kDa
src_method	syn
entity_count	1

Entity 12 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	2156

▶

6. Citations (1)

▶

length_a	109.349 Å
length_b	172.078 Å
length_c	113.144 Å
angle_alpha	90.00 °
angle_beta	97.64 °
angle_gamma	90.00 °
z_pdb	10

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.960 Å
resolution_low	91.870 Å
r_factor	0.1889
r_work	0.1874
r_free	0.2182

fit	/app/data/saxs_computation/rm/9rm2/9rm2.fit
pddf	/app/data/pr_computation/rm/9rm2/9rm2.pr.out
profile	/app/data/saxs_computation/rm/9rm2/9rm2.dat

BKPyV VP1 IN COMPLEX WITH 319C07-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

Diffraction

5. Entities & Polymer Info (12)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 non-polymer

Entity 9 non-polymer

Entity 10 non-polymer

Entity 11 non-polymer

Entity 12 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)