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9wtk

Crystal structure of monoalkyl phthalate hydrolase in complex with MBP from Rhodococcus sp. EG-5

Method: X-RAY DIFFRACTION D_max: 225.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9wtk
deposition_date	2025-09-16
last_revision	2026-05-27
title	Crystal structure of monoalkyl phthalate hydrolase in complex with MBP from Rhodococcus sp. EG-5
keywords	Mono-butyl phthalate, 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	69.00 Å
rg_electron	69.65 Å
i0	1442650000.00
molecular_weight	325130.0 kDa
excluded_volume	409150 Å³
envelope_volume	608010 Å³
shell_volume	79478 Å³
envelope_diameter	251.3 Å
shell_rg	60.67 Å
envelope_rg	68.16 Å
shape_rg	69.65 Å
total_rg	69.45 Å
total_atoms	22922
n_residues	2905
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	225.9 Å
rg_real	69.50 Å
rg_real_error	2.55 Å
i0_real	1.4420e+09
i0_real_error	3.6770e+07
rg_reciprocal	66.84 Å
i0_reciprocal	1435000000.0000
total_estimate	0.7981
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	49.1 Å
skewness	0.572
kurtosis	-0.328
angular_range	— – 0.1150 Å⁻¹
current_alpha	0.0009
highest_alpha	39050000.0000
n_real_points	24
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.818; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.732; Smooth: 0.188

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	Mono-ethylhexylphthalate hydrolase
formula_weight	33066.5 kDa
src_method	man
entity_count	10

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F,G,H,I,J
atom_count	22926

MNTDLSVNYISVGGIRTRYIDQGEGPVILLIHGGHSGMSMPVGGDGWAPVIAPLVDKGFRVVTFDKLGQGETDLAPTHAEWTFDAVVKHARGFIDALGLEDMILVGHSRGGLLASKLALDMPESTKGLFIVSSATLAGTDAKFRDVEFYDAITRSLPADASPEEICGAYFRALYVTPVPQEQINAAAAKYVKENHQNALKTYPMVEKKYWEPSLQAAKDDIRARLFAGEVNIPVEVVWGRDDRSAPVDLGIAFYQKLALVSETTSLHILGTAGHNVFAERTEDFVRILADYAGRRSASYATRR

Source

organism	Rhodococcus sp. EG-5
ncbi_taxonomy_id	1747801
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	syn
entity_count	44

Entity 3 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	61

Entity 4 non-polymer

description	PHTHALIC ACID
formula_weight	166.1 kDa
src_method	syn
entity_count	10

Entity 5 non-polymer

description	1-BUTANOL
formula_weight	74.1 kDa
src_method	syn
entity_count	3

Entity 6 non-polymer

description	MALONATE ION
formula_weight	102.0 kDa
src_method	syn
entity_count	2

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	4

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6. Citations (1)

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length_a	176.313 Å
length_b	244.890 Å
length_c	192.097 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	80

space_group	C 2 2 2
int_tables_number	21
crystal_system	orthorhombic

resolution	2.800 Å
resolution_low	24.290 Å
r_factor	0.2584
r_work	0.2569
r_free	0.2864

fit	/app/data/saxs_computation/wt/9wtk/9wtk.fit
pddf	/app/data/pr_computation/wt/9wtk/9wtk.pr.out
profile	/app/data/saxs_computation/wt/9wtk/9wtk.dat