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9r7f

De novo designed enzyme for the Morita-Baylis-Hillman reaction (MBH48)

Method: X-RAY DIFFRACTION D_max: 59.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9r7f
deposition_date	2025-05-14
title	De novo designed enzyme for the Morita-Baylis-Hillman reaction (MBH48)
keywords	Morita-Baylis-Hillman enzyme, DE NOVO PROTEIN; DE NOVO PROTEIN
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	18.44 Å
rg_electron	17.38 Å
i0	8851220.00
molecular_weight	22091.0 kDa
excluded_volume	27764 Å³
envelope_volume	31838 Å³
shell_volume	15689 Å³
envelope_diameter	59.9 Å
shell_rg	23.05 Å
envelope_rg	17.49 Å
shape_rg	17.36 Å
total_rg	18.35 Å
total_atoms	1550
n_residues	201
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	59.0 Å
rg_real	18.38 Å
rg_real_error	0.39 Å
i0_real	8.8510e+06
i0_real_error	1.0910e+05
rg_reciprocal	18.39 Å
i0_reciprocal	8851000.0000
total_estimate	0.8126
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	23.4 Å
skewness	0.253
kurtosis	-0.337
angular_range	— – 0.4300 Å⁻¹
current_alpha	0.0000
highest_alpha	1444000.0000
n_real_points	74
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.855; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	MBH48
formula_weight	23319.4 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	1649

MGSSHHHHHHSSGENLYFQSGGAGAALGRRLLGAILGGDPREGLALAKRLYEGLWMLGVDPERGEAILAEVRAATGLDAEIDALAAVMRALNATIIAADEELRAADPAAYAAVLTFADLVLTSKLYPEKVSPEEKKAAELFLKGEELIAEYLRGGPESYLTKGKEYVAEAAKILGLDPAQAWRGAVVHVAGSVARTPEQAAALAALDRTFEEALAAAEARL

Source

organism	synthetic construct
ncbi_taxonomy_id	32630
host_organism	Escherichia coli

Entity 2 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	9

Entity 3 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	88

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6. Citations (1)

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length_a	76.056 Å
length_b	76.056 Å
length_c	59.638 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	6

space_group	P 63
int_tables_number	173
crystal_system	hexagonal

resolution	1.930 Å
resolution_low	44.210 Å
r_factor	0.2040
r_work	0.2014
r_free	0.2517

fit	/app/data/saxs_computation/r7/9r7f/9r7f.fit
pddf	/app/data/pr_computation/r7/9r7f/9r7f.pr.out
profile	/app/data/saxs_computation/r7/9r7f/9r7f.dat

De novo designed enzyme for the Morita-Baylis-Hillman reaction (MBH48)

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