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9vd8

Structure of a truncated loopA mutant from the human gut flora K. grimontii Apg in complex with glucose

Method: X-RAY DIFFRACTION D_max: 85.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vd8
deposition_date	2025-06-07
last_revision	2025-09-03
title	Structure of a truncated loopA mutant from the human gut flora K. grimontii Apg in complex with glucose
keywords	Hydrolase, Complex; 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	26.21 Å
rg_electron	25.08 Å
i0	71845300.00
molecular_weight	66128.0 kDa
excluded_volume	82481 Å³
envelope_volume	96274 Å³
shell_volume	31558 Å³
envelope_diameter	87.5 Å
shell_rg	32.85 Å
envelope_rg	25.42 Å
shape_rg	25.09 Å
total_rg	25.87 Å
total_atoms	4684
n_residues	583
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	85.2 Å
rg_real	26.17 Å
rg_real_error	0.49 Å
i0_real	7.1850e+07
i0_real_error	1.0240e+06
rg_reciprocal	26.19 Å
i0_reciprocal	71850000.0000
total_estimate	0.8916
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	30.7 Å
skewness	0.332
kurtosis	-0.320
angular_range	— – 0.3050 Å⁻¹
current_alpha	0.0000
highest_alpha	15480000.0000
n_real_points	62
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.875; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.963

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Apg-truncated loopA
formula_weight	67404.9 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	4913

MLKAWHLPVAPFIKEQQERLMITLWLSGDDLPPRVTLRAEEDNEELSLPMHRLRQAPHPGVVAWRGEINLVNGQPRRRYSFKLLWADRQLWFTPQEFNRFPPARLEQFAVDLPDSGPQWVADQVFYQIFPDRFARSQSHDIVRKAWDEPLTAEAGGSTFYGGDLDGISEKLPYLKQLGVTALYLNPVFVAPSVHKYDTEDYRRVDPQFGGDAALLRLRHNTQKEGMRLILDGVFNHSGDSHAWFDRHQRGSGGACHNADSPWRDWYNFSPEGVAHDWLGYASLPKLDYRSSTLIDEIYGGEDSVVRHWLKAPWSMDGWRLDVVHMLGEGGGARNNLRHIAGITQAAKLERPDAFVFGEHFGDARQWLQADVEDSAMNYRGFTFPLWGFLANTDISYDPQKIDAQTCMAWMDNYRAGLSHQQQLRMFNQLDSHDTARFKSLLGKDVARLPLAVVWLFSWPGVPCIYYGDEVGVDGNNDPFCRKPFPWDPALQDGDLLDLYKRMSKLRKAHQALRYGGCQVIYAEDNVVVFVRVYKQQRVLVAINRGEACEVVIEDSPLLDVNGWQLKEGAGALHDGVLTLPAISASVWFSR

Source

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

Entity 2 non-polymer

description	alpha-D-glucopyranose
formula_weight	180.2 kDa
src_method	syn
entity_count	1

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	229

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6. Citations (1)

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length_a	75.870 Å
length_b	75.870 Å
length_c	401.959 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	12

space_group	P 65 2 2
int_tables_number	179
crystal_system	hexagonal

resolution	2.390 Å
resolution_low	46.910 Å
r_factor	0.1934
r_work	0.1911
r_free	0.2365

fit	/app/data/saxs_computation/vd/9vd8/9vd8.fit
pddf	/app/data/pr_computation/vd/9vd8/9vd8.pr.out
profile	/app/data/saxs_computation/vd/9vd8/9vd8.dat

Structure of a truncated loopA mutant from the human gut flora K. grimontii Apg in complex with glucose

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