← Back to search

1eb8

Structure Determinants of Substrate Specificity of Hydroxynitrile Lyase from Manihot esculenta

Method: X-RAY DIFFRACTION D_max: 80.0 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	1eb8
deposition_date	2001-07-24
title	Structure Determinants of Substrate Specificity of Hydroxynitrile Lyase from Manihot esculenta
keywords	HYDROXYNITRILE LYASE, SUBSTRATE SPECIFICITY, ACTIVE-SITE TUNNEL MUTANT, LYASE; LYASE
method	X-RAY DIFFRACTION

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	25.39 Å
rg_electron	24.48 Å
i0	53284700.00
molecular_weight	59166.0 kDa
excluded_volume	75014 Å³
envelope_volume	83856 Å³
shell_volume	28381 Å³
envelope_diameter	84.6 Å
shell_rg	31.99 Å
envelope_rg	24.64 Å
shape_rg	24.49 Å
total_rg	25.27 Å
total_atoms	4176
n_residues	520
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

▼

3. P(r) Analysis (GNOM)

dmax	80.0 Å
rg_real	25.36 Å
rg_real_error	0.47 Å
i0_real	5.3280e+07
i0_real_error	8.2660e+05
rg_reciprocal	25.37 Å
i0_reciprocal	53290000.0000
total_estimate	0.9010
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	27.9 Å
skewness	0.326
kurtosis	-0.462
angular_range	— – 0.3150 Å⁻¹
current_alpha	0.0000
highest_alpha	12810000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.908; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.991

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (3)

Entity 1 polymer

description	(S)-ACETONE-CYANOHYDRIN LYASE
formula_weight	29720.1 kDa
ec_number	4.2.1.37
mutation	YES
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	4426

PISKMVTAHFVLIHTICHGAWIWHKLKPALERAGHKVTALDMAASGIDPRQIEQINSFDEYSEPLLTFLEKLPQGEKVIIVGESCAGLNIAIAADRYVDKIAAGVFHNSLLPDTVHSPSYTVEKLLESFPDARDTEYFTFTNITGETITTMKLGFVLLRENLFTKCTDGEYELAKMVMRKGSLFQNVLAQRPKFTEKGYGSIKKVYIWTDQDKIFLPDFQRWQIANYKPDKVYQVQGGDHKLQLTKTEEVAHILQEVADAYA

Source

organism	MANIHOT ESCULENTA
common_name	CASSAVA
ncbi_taxonomy_id	3983
host_organism	ESCHERICHIA COLI

Entity 2 non-polymer

description	(4S)-2-METHYL-2,4-PENTANEDIOL
formula_weight	118.2 kDa
src_method	syn
entity_count	2

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	250

▶

6. Citations (2)

▶

length_a	106.400 Å
length_b	106.400 Å
length_c	188.430 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	P 41 21 2
int_tables_number	92
crystal_system	—

resolution	2.100 Å
resolution_low	8.000 Å
r_factor	0.1920
r_work	0.1920
r_free	0.2340

fit	/app/data/saxs_computation/eb/1eb8/1eb8.fit
pddf	/app/data/pr_computation/eb/1eb8/1eb8.pr.out
profile	/app/data/saxs_computation/eb/1eb8/1eb8.dat

Structure Determinants of Substrate Specificity of Hydroxynitrile Lyase from Manihot esculenta

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