Structure of truncated loopA and loopB mutants from the human gut flora K. grimontii Apg

Method: X-RAY DIFFRACTION D_max: 159.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vdw
deposition_date	2025-06-09
last_revision	2025-09-03
title	Structure of truncated loopA and loopB mutants 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	45.15 Å
rg_electron	45.32 Å
i0	613843000.00
molecular_weight	209180.0 kDa
excluded_volume	263480 Å³
envelope_volume	342790 Å³
shell_volume	64540 Å³
envelope_diameter	169.5 Å
shell_rg	48.15 Å
envelope_rg	44.82 Å
shape_rg	45.32 Å
total_rg	45.46 Å
total_atoms	14816
n_residues	1855
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	159.1 Å
rg_real	45.46 Å
rg_real_error	1.75 Å
i0_real	6.1380e+08
i0_real_error	1.1980e+07
rg_reciprocal	45.15 Å
i0_reciprocal	613600000.0000
total_estimate	0.8426
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	45.5 Å
skewness	0.524
kurtosis	-0.172
angular_range	— – 0.1750 Å⁻¹
current_alpha	0.0000
highest_alpha	83900000.0000
n_real_points	36
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.767; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.841; Smooth: 0.809

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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	62.210 Å
length_b	70.893 Å
length_c	130.330 Å
angle_alpha	87.64 °
angle_beta	79.98 °
angle_gamma	89.93 °
z_pdb	4

space_group	P 1
int_tables_number	1
crystal_system	triclinic

resolution	2.380 Å
resolution_low	35.420 Å
r_factor	0.2012
r_work	0.1988
r_free	0.2473

description	Acarbose hydrolase
formula_weight	62097.2 kDa
src_method	man
entity_count	4

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	15322

Structure of truncated loopA and loopB mutants 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	486

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