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9ti2

Crystal structure of the zinc-containing Phosphotriesterase dPTE2-H55(pi)MH

Method: X-RAY DIFFRACTION D_max: 171.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ti2
deposition_date	2025-12-04
title	Crystal structure of the zinc-containing Phosphotriesterase dPTE2-H55(pi)MH
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	48.32 Å
rg_electron	48.69 Å
i0	691694000.00
molecular_weight	215310.0 kDa
excluded_volume	268530 Å³
envelope_volume	347610 Å³
shell_volume	62804 Å³
envelope_diameter	171.8 Å
shell_rg	48.59 Å
envelope_rg	48.08 Å
shape_rg	48.69 Å
total_rg	48.70 Å
total_atoms	29992
n_residues	1944
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	171.7 Å
rg_real	48.69 Å
rg_real_error	1.84 Å
i0_real	6.9170e+08
i0_real_error	1.2870e+07
rg_reciprocal	48.32 Å
i0_reciprocal	691400000.0000
total_estimate	0.8387
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	57.2 Å
skewness	0.471
kurtosis	-0.262
angular_range	— – 0.1650 Å⁻¹
current_alpha	0.0000
highest_alpha	47250000.0000
n_real_points	34
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.737; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.914; Smooth: 0.773

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Parathion hydrolase
formula_weight	37249.9 kDa
ec_number	3.1.8.1
mutation	H55(pi)MH
src_method	man
entity_count	6

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F
atom_count	30693

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	12

Entity 3 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	12

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	701

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6. Citations (1)

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length_a	442.553 Å
length_b	57.931 Å
length_c	84.463 Å
angle_alpha	90.00 °
angle_beta	100.88 °
angle_gamma	90.00 °
z_pdb	24

space_group	C 1 2 1
int_tables_number	5
crystal_system	monoclinic

resolution	1.690 Å
resolution_low	19.900 Å
r_factor	0.2045
r_work	0.2039
r_free	0.2164

fit	/app/data/saxs_computation/ti/9ti2/9ti2.fit
pddf	/app/data/pr_computation/ti/9ti2/9ti2.pr.out
profile	/app/data/saxs_computation/ti/9ti2/9ti2.dat

Crystal structure of the zinc-containing Phosphotriesterase dPTE2-H55(pi)MH

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