Crystal structure of AcvB from Agrobacterium tumefaciens

Method: X-RAY DIFFRACTION D_max: 126.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9xhm
deposition_date	2025-11-01
title	Crystal structure of AcvB from Agrobacterium tumefaciens
keywords	Lysyl-phosphatidylglycerol hydrolase, 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	36.27 Å
rg_electron	36.11 Å
i0	115955000.00
molecular_weight	87995.0 kDa
excluded_volume	110900 Å³
envelope_volume	147610 Å³
shell_volume	36554 Å³
envelope_diameter	132.2 Å
shell_rg	39.26 Å
envelope_rg	35.86 Å
shape_rg	36.13 Å
total_rg	36.24 Å
total_atoms	6195
n_residues	844
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	126.6 Å
rg_real	36.62 Å
rg_real_error	1.29 Å
i0_real	1.1600e+08
i0_real_error	2.0630e+06
rg_reciprocal	36.41 Å
i0_reciprocal	115900000.0000
total_estimate	0.8106
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	28.8 Å
skewness	0.542
kurtosis	-0.248
angular_range	— – 0.2200 Å⁻¹
current_alpha	0.0000
highest_alpha	65240000.0000
n_real_points	45
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.729; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.692; Smooth: 0.653

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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	66.565 Å
length_b	76.273 Å
length_c	77.219 Å
angle_alpha	113.86 °
angle_beta	98.35 °
angle_gamma	106.78 °
z_pdb	2

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	3.130 Å
resolution_low	40.600 Å
r_factor	0.2272
r_work	0.2245
r_free	0.2800

description	AcvB
formula_weight	46754.7 kDa
src_method	man
entity_count	2

type	polypeptide(L)
strand_id	A,B
atom_count	6195

Crystal structure of AcvB from Agrobacterium tumefaciens

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 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)

organism	Agrobacterium tumefaciens
ncbi_taxonomy_id	358
host_organism	Escherichia coli BL21(DE3)

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

fit	/app/data/saxs_computation/xh/9xhm/9xhm.fit
pddf	/app/data/pr_computation/xh/9xhm/9xhm.pr.out
profile	/app/data/saxs_computation/xh/9xhm/9xhm.dat