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9qrm

X-ray structure of Kp32gp38 in complex with K21 pyr5

Method: X-RAY DIFFRACTION D_max: 133.7 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qrm
deposition_date	2025-04-03
title	X-ray structure of Kp32gp38 in complex with K21 pyr5
keywords	Klebsiella pneumoniae, phage depolymerase, protein structure, CPS degradation, immune response induction, VIRAL PROTEIN; VIRAL PROTEIN
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	34.10 Å
rg_electron	34.56 Å
i0	115093000.00
molecular_weight	56305.0 kDa
excluded_volume	53934 Å³
envelope_volume	98439 Å³
shell_volume	26818 Å³
envelope_diameter	139.3 Å
shell_rg	35.50 Å
envelope_rg	35.75 Å
shape_rg	34.53 Å
total_rg	34.67 Å
total_atoms	4258
n_residues	563
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	133.7 Å
rg_real	34.71 Å
rg_real_error	2.03 Å
i0_real	1.1510e+08
i0_real_error	2.1280e+06
rg_reciprocal	34.33 Å
i0_reciprocal	115100000.0000
total_estimate	0.7009
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	26.2 Å
skewness	0.726
kurtosis	-0.024
angular_range	— – 0.2300 Å⁻¹
current_alpha	0.0000
highest_alpha	6394000.0000
n_real_points	47
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.323; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.192; Smooth: 0.947

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Depolymerase 2, capsule K21-specific
formula_weight	62754.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B
atom_count	4929

MLDNFNQPKGSTIGVLKDGRTIQEAFDSLPRLESFSGSTATDKLRAAITLGVSEVAIGPVEGNGGRPYEFGDVVIPYPLRIVGCGSQGINVTKGTVLKRSAGASFMFHFTGEGQAQRPMGGGLFNINLNGDTATALGDIIKVTQWSYFKANNCAFQNMAGWGIRLKDVMESNISGNLFRRLGGPSGGGILFDDVRSAVTDNVNNLHIEDNTFALMSGPWIGSTANSNPDLIWIVRNKFEFDGTPAAPNTVDSYVLDFQQLSRAFIQDNGFTHFTTERNRYVGVLRVGATAVGTIKFEDNLLFACESAGLIAGGIVVSRGNVNNQGSATTAIKQFTNTSSKLCKLERVINVQSNGNVSVGQQILPDGYINMAELPGNTRLPSEYDADGETTSVLRVPANTQVRQWSVPKMYKDGLTVTKVTVRAKGAAAGAILSLQSGSTVLSTKSIDAGVWKNYVFYVKANQLQETLQLRNTGTADVLADGMVFGKVDYIDWDFAIAPGTLAAGAKYTTPNQSYLDVAGMRVQAVSIPMFDGPTTGLQVWVEATSANGSFVVVMKNDTGSELVTTVTRCRVRAFVSKGHHHHHH

Source

organism	Klebsiella pneumoniae
ncbi_taxonomy_id	573
host_organism	Escherichia coli

Entity 2 branched

description	;(2~{S},4~{a}~{S},6~{R},7~{S},8~{R},8~{a}~{R})-2-methyl-6,7,8-tris(oxidanyl)-4,4~{a},6,7,8,8~{a}-hexahydropyrano[3,2-d][1,3]dioxine-2-carboxylic acid-(4-4)-beta-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-galactopyranose ;
formula_weight	898.8 kDa
src_method	man
entity_count	1

Entity 3 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	nat
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	509

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6. Citations (1)

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length_a	70.492 Å
length_b	70.492 Å
length_c	205.594 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	6

space_group	P 3 2 1
int_tables_number	150
crystal_system	—

resolution	1.800 Å
resolution_low	14.940 Å
r_factor	0.1907
r_work	0.1882
r_free	0.2354

fit	/app/data/saxs_computation/qr/9qrm/9qrm.fit
pddf	/app/data/pr_computation/qr/9qrm/9qrm.pr.out
profile	/app/data/saxs_computation/qr/9qrm/9qrm.dat