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9qde

;Crystal structure of the non-glycosylated polyester hydrolase Leipzig 7 (PHL7) mut3 variant expressed in Pichia pastoris (P_PHL7mut3_ng) ;

Method: X-RAY DIFFRACTION D_max: 54.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qde
deposition_date	2025-03-06
title	;Crystal structure of the non-glycosylated polyester hydrolase Leipzig 7 (PHL7) mut3 variant expressed in Pichia pastoris (P_PHL7mut3_ng) ;
keywords	E. coli, LCC, K. phaffii, PETase, P. pastoris, 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	17.90 Å
rg_electron	16.65 Å
i0	15052600.00
molecular_weight	28298.0 kDa
excluded_volume	34963 Å³
envelope_volume	37900 Å³
shell_volume	18468 Å³
envelope_diameter	53.8 Å
shell_rg	23.40 Å
envelope_rg	16.90 Å
shape_rg	16.64 Å
total_rg	17.63 Å
total_atoms	3914
n_residues	261
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	54.1 Å
rg_real	17.72 Å
rg_real_error	0.23 Å
i0_real	1.5050e+07
i0_real_error	1.5600e+05
rg_reciprocal	17.74 Å
i0_reciprocal	15050000.0000
total_estimate	0.8203
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	24.1 Å
skewness	0.014
kurtosis	-0.538
angular_range	— – 0.4450 Å⁻¹
current_alpha	0.0000
highest_alpha	6191000.0000
n_real_points	75
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.900; Stabil: 0.996; Sysdev: 1.000; Positv: 1.000; Valcen: 0.973; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Polyester Hydrolase Leipzig 7 (PHL-7), catalysis-deficient S131A mutant
formula_weight	28727.9 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	4598

ANPYERGPDPTESSIEAVRGPFAVAQTTVSRLQADGFGGGTIYYPTDTSQGTFGAVAISPGFTAGQESIAWLGPRIASQGFVVITIDTITRLDQPDSRGRQLQAALDHLRTNSVVRNRIDPNRMAVMGHSMGGGGALSAAAQQTSLEAAIPLQGWHTRKQWSSVRTPTLVVGAELDTIAPVSSHSEAFYNSLPSDLDKAYMELRGASHTVSNTPDTTTAKYSIAWLKRFVDKDLRYEQFLCPAPDDFAISEYRSTCPFHHHHHH

Source

organism	compost metagenome
ncbi_taxonomy_id	702656
host_organism	Pichia

Entity 2 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	1

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	443

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6. Citations (1)

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length_a	46.052 Å
length_b	59.014 Å
length_c	86.151 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	1.020 Å
resolution_low	27.920 Å
r_factor	0.1243
r_work	0.1238
r_free	0.1496

fit	/app/data/saxs_computation/qd/9qde/9qde.fit
pddf	/app/data/pr_computation/qd/9qde/9qde.pr.out
profile	/app/data/saxs_computation/qd/9qde/9qde.dat

;Crystal structure of the non-glycosylated polyester hydrolase Leipzig 7 (PHL7) mut3 variant expressed in Pichia pastoris (P_PHL7mut3_ng) ;

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