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9r6w

CHAP domain of Pneumococcal Endopeptidase PcsB

Method: X-RAY DIFFRACTION D_max: 77.1 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9r6w
deposition_date	2025-05-13
last_revision	2026-05-27
title	CHAP domain of Pneumococcal Endopeptidase PcsB
keywords	Peptidoglycan, Pneumococcus, Division, HYDROLASE; HYDROLASE
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	24.26 Å
rg_electron	23.55 Å
i0	39573200.00
molecular_weight	46759.0 kDa
excluded_volume	57530 Å³
envelope_volume	68244 Å³
shell_volume	24419 Å³
envelope_diameter	77.5 Å
shell_rg	30.22 Å
envelope_rg	23.50 Å
shape_rg	23.55 Å
total_rg	24.31 Å
total_atoms	3311
n_residues	439
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	77.1 Å
rg_real	24.22 Å
rg_real_error	0.50 Å
i0_real	3.9570e+07
i0_real_error	5.7650e+05
rg_reciprocal	24.23 Å
i0_reciprocal	39570000.0000
total_estimate	0.9050
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	28.1 Å
skewness	0.282
kurtosis	-0.465
angular_range	— – 0.3250 Å⁻¹
current_alpha	0.0000
highest_alpha	10200000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.933; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.976

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Peptidoglycan hydrolase PcsB
formula_weight	14673.9 kDa
ec_number	3.2.1.-
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	AAA,BBB,CCC,DDD
atom_count	3623

MGSSHHHHHHSSGLVPRGSAKVRPTYSTNASSYPIGECTWGVKTLAPWAGDYWGNGAQWATSAAAAGFRTGSTPQVGAIACWNDGGYGHVAVVTAVESTTRIQVSESNYAGNRTIGNHRGWFNPTTTSEGFVTYIYAD

Source

organism	Streptococcus pneumoniae
ncbi_taxonomy_id	1313
host_organism	Escherichia coli

Entity 2 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	7

Entity 3 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	258

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6. Citations (1)

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length_a	84.280 Å
length_b	117.380 Å
length_c	47.690 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	P 21 21 2
int_tables_number	18
crystal_system	—

resolution	1.700 Å
resolution_low	44.222 Å
r_factor	—
r_work	0.1719
r_free	0.1941

fit	/app/data/saxs_computation/r6/9r6w/9r6w.fit
pddf	/app/data/pr_computation/r6/9r6w/9r6w.pr.out
profile	/app/data/saxs_computation/r6/9r6w/9r6w.dat

CHAP domain of Pneumococcal Endopeptidase PcsB

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