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9vzr

MG8, a PET hydrolase enzyme from the human saliva metagenome

Method: X-RAY DIFFRACTION D_max: 57.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vzr
deposition_date	2025-07-23
last_revision	2026-01-28
title	MG8, a PET hydrolase enzyme from the human saliva metagenome
keywords	polyethylene terephthalate, PET 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	18.22 Å
rg_electron	16.92 Å
i0	15557900.00
molecular_weight	29062.0 kDa
excluded_volume	35994 Å³
envelope_volume	38669 Å³
shell_volume	18602 Å³
envelope_diameter	59.1 Å
shell_rg	23.64 Å
envelope_rg	17.23 Å
shape_rg	16.89 Å
total_rg	17.92 Å
total_atoms	2046
n_residues	271
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	57.9 Å
rg_real	18.08 Å
rg_real_error	0.25 Å
i0_real	1.5560e+07
i0_real_error	1.8100e+05
rg_reciprocal	18.10 Å
i0_reciprocal	15560000.0000
total_estimate	0.8866
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	24.3 Å
skewness	0.061
kurtosis	-0.464
angular_range	— – 0.4350 Å⁻¹
current_alpha	0.0000
highest_alpha	4944000.0000
n_real_points	75
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.849; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.992

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	PET hydrolase, MG8
formula_weight	29759.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2254

NNPPPPDDPGAPSPYQRGPDPTVSFVEASRGNYRVATSNVSSLVSGFGGGTIHYPSNATGTMGAIVVIPGYVSGEGSIDWWGPKLASYGFVVMTIGTNSGFDQPPSRARQINNALDYLVEQNTRTGSPVRGMIDPSRLGVIGWSMGGGGTIRVAGEGRIKAAIPLAPWDTSSIPSRGVQAPTLIFACQSDVVAPVRSHASPFYNALPGSISKAFVNLNNGNHFCANGGSSFGRYDAALGRLGVSWMKRFLDEDRRYSQFLCGPNHTGDRQITEYRGNCPY

Source

organism	Pseudomonas sp.
ncbi_taxonomy_id	306
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	3

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	208

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6. Citations (1)

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length_a	51.410 Å
length_b	61.009 Å
length_c	69.647 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 21
int_tables_number	19
crystal_system	orthorhombic

resolution	1.200 Å
resolution_low	28.830 Å
r_factor	0.1336
r_work	0.1328
r_free	0.1604

fit	/app/data/saxs_computation/vz/9vzr/9vzr.fit
pddf	/app/data/pr_computation/vz/9vzr/9vzr.pr.out
profile	/app/data/saxs_computation/vz/9vzr/9vzr.dat