← Back to search

9vpf

Crystal structure of D-aspartate oxidase from Cryptococcus humicola UJ1.

Method: X-RAY DIFFRACTION D_max: 111.2 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9vpf
deposition_date	2025-07-03
title	Crystal structure of D-aspartate oxidase from Cryptococcus humicola UJ1.
keywords	D-amino acid, OXIDOREDUCTASE; OXIDOREDUCTASE
method	X-RAY DIFFRACTION

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	37.53 Å
rg_electron	36.54 Å
i0	389684000.00
molecular_weight	156510.0 kDa
excluded_volume	194100 Å³
envelope_volume	250230 Å³
shell_volume	54661 Å³
envelope_diameter	111.2 Å
shell_rg	45.53 Å
envelope_rg	35.16 Å
shape_rg	36.54 Å
total_rg	37.06 Å
total_atoms	11023
n_residues	1437
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	111.2 Å
rg_real	37.26 Å
rg_real_error	0.72 Å
i0_real	3.8970e+08
i0_real_error	5.6910e+06
rg_reciprocal	37.43 Å
i0_reciprocal	389700000.0000
total_estimate	0.9055
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	55.6 Å
skewness	-0.042
kurtosis	-0.769
angular_range	— – 0.2100 Å⁻¹
current_alpha	0.0000
highest_alpha	109200000.0000
n_real_points	43
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.951; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.919

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (4)

Entity 1 polymer

description	D-aspartate oxidase
formula_weight	39503.9 kDa
ec_number	1.4.3.1
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	12326

MPPSDPIIVLGAGVIGLTTAVRLLEAHLGANVHILADHWPSDALDAQYASTIAGAHHLSFADDGDARQRRWDMRTFDVLYDEWKAVGERTGLMALTQTEMWEGATSHLAVYEGNPDFRVLDPRTAPCSNITHMVSFTSLTIAPTVYLAALEARVRDLGAKLHRAHVPSLGALRTDPALLALYTRPPAAVFVCAGLGARHLVPAPEAAALFPTRGQVVVVRAPWMRAGFTRQVGSLGGGEGGTRTYIIPRCNGEVVLGGTMEQGDWTPYPRDETVTDILTRALQICPDIAPPYARSWPKDDQVAALRSIVVRDAVGFRPSRAGGARVALASAAGMRVVYNYGHGGAGWQSCWGCAEDAVALWAGGAGGARL

Source

organism	Vanrija humicola
ncbi_taxonomy_id	5417
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	FLAVIN-ADENINE DINUCLEOTIDE
formula_weight	785.5 kDa
src_method	syn
entity_count	4

Entity 3 non-polymer

description	FLUORIDE ION
formula_weight	19.0 kDa
src_method	syn
entity_count	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	1303

▶

6. Citations (1)

▶

length_a	84.983 Å
length_b	109.338 Å
length_c	189.401 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	1.700 Å
resolution_low	47.350 Å
r_factor	0.1909
r_work	0.1896
r_free	0.2156

fit	/app/data/saxs_computation/vp/9vpf/9vpf.fit
pddf	/app/data/pr_computation/vp/9vpf/9vpf.pr.out
profile	/app/data/saxs_computation/vp/9vpf/9vpf.dat

Crystal structure of D-aspartate oxidase from Cryptococcus humicola UJ1.

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