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9ti1

Crystal structure of the zinc-containing Phosphotriesterase dPTE2-H55

Method: X-RAY DIFFRACTION D_max: 102.4 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ti1
deposition_date	2025-12-04
title	Crystal structure of the zinc-containing Phosphotriesterase dPTE2-H55
keywords	Phosphotriesterase, Zinc-dependent, 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	27.51 Å
rg_electron	26.88 Å
i0	85639300.00
molecular_weight	71983.0 kDa
excluded_volume	89718 Å³
envelope_volume	102640 Å³
shell_volume	32002 Å³
envelope_diameter	96.1 Å
shell_rg	34.18 Å
envelope_rg	27.00 Å
shape_rg	26.89 Å
total_rg	27.57 Å
total_atoms	10045
n_residues	653
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	102.4 Å
rg_real	27.58 Å
rg_real_error	0.91 Å
i0_real	8.5640e+07
i0_real_error	1.2750e+06
rg_reciprocal	27.56 Å
i0_reciprocal	85640000.0000
total_estimate	0.7408
solution_quality	REASONABLE a REASONABLE solution
n_peaks	3
r_peak_primary	30.0 Å
skewness	0.436
kurtosis	-0.326
angular_range	— – 0.2900 Å⁻¹
current_alpha	0.0000
highest_alpha	56880000.0000
n_real_points	59
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.588; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.862; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Parathion hydrolase
formula_weight	37236.9 kDa
ec_number	3.1.8.1
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	10452

SNIGSGITNSGDRINTVRGPITISEAGFTLMHEHICGSSAGFLRAWPEFFGSRDALAEKAVRGLRRARAAGVRTIVDVSTFDIGRDVELLAEVSEAADVHIVAATGLWFDPPLSMRLRSVEELTQFFLREIQYGIEDTGIRAGIIKVATTGKATPFQERVLRAAARASLATGVPVTTHTDASQRDGEQQADIFESEGLDPSRVCIGHSDDTDDLDYLTALAARGYLIGLDHIPHSAIGLEDNASAAALLGLRSWQTRALLIKALIDQGYADQILVSNDWLFGFSSYVTNIMDVMDRVNPDGMAFIPLRVIPFLREKGVPDETLETIMVDNPARFLSPTLRAS

Source

organism	Brevundimonas diminuta
ncbi_taxonomy_id	293
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	4

Entity 3 non-polymer

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

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	407

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6. Citations (1)

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length_a	63.486 Å
length_b	69.979 Å
length_c	154.161 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 21 21 21
int_tables_number	19
crystal_system	orthorhombic

resolution	1.550 Å
resolution_low	19.690 Å
r_factor	0.1780
r_work	0.1775
r_free	0.1872

fit	/app/data/saxs_computation/ti/9ti1/9ti1.fit
pddf	/app/data/pr_computation/ti/9ti1/9ti1.pr.out
profile	/app/data/saxs_computation/ti/9ti1/9ti1.dat

Crystal structure of the zinc-containing Phosphotriesterase dPTE2-H55

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