Structure of a truncated loopB mutant from the human gut flora K. grimontii Apg

Method: X-RAY DIFFRACTION D_max: 155.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vdg
deposition_date	2025-06-08
last_revision	2025-09-03
title	Structure of a truncated loopB mutant from the human gut flora K. grimontii Apg
keywords	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	44.97 Å
rg_electron	45.10 Å
i0	596724000.00
molecular_weight	205220.0 kDa
excluded_volume	257930 Å³
envelope_volume	335230 Å³
shell_volume	63540 Å³
envelope_diameter	165.8 Å
shell_rg	48.00 Å
envelope_rg	44.37 Å
shape_rg	45.10 Å
total_rg	45.23 Å
total_atoms	14537
n_residues	1843
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	155.8 Å
rg_real	45.25 Å
rg_real_error	1.56 Å
i0_real	5.9670e+08
i0_real_error	1.0820e+07
rg_reciprocal	44.97 Å
i0_reciprocal	596500000.0000
total_estimate	0.8489
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	44.5 Å
skewness	0.507
kurtosis	-0.206
angular_range	— – 0.1750 Å⁻¹
current_alpha	0.0000
highest_alpha	79800000.0000
n_real_points	36
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.805; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.869; Smooth: 0.748

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

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6. Citations (1)

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length_a	62.364 Å
length_b	70.890 Å
length_c	130.304 Å
angle_alpha	92.54 °
angle_beta	100.14 °
angle_gamma	90.08 °
z_pdb	4

space_group	P 1
int_tables_number	1
crystal_system	triclinic

resolution	2.670 Å
resolution_low	48.620 Å
r_factor	0.2407
r_work	0.2392
r_free	0.2690

description	APG-truncated loopB
formula_weight	63845.0 kDa
src_method	man
entity_count	4

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	14849

Structure of a truncated loopB mutant from the human gut flora K. grimontii Apg

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 (2)

Entity 1 polymer

Polymer

Source

Entity 2 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)

organism	Klebsiella grimontii
ncbi_taxonomy_id	2058152
host_organism	Escherichia coli BL21(DE3)

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	312

fit	/app/data/saxs_computation/vd/9vdg/9vdg.fit
pddf	/app/data/pr_computation/vd/9vdg/9vdg.pr.out
profile	/app/data/saxs_computation/vd/9vdg/9vdg.dat