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9qgz

Crystal structure of a D-lactate dehydrogenase from Porcellio dilatatus

Method: X-RAY DIFFRACTION D_max: 180.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qgz
deposition_date	2025-03-14
title	Crystal structure of a D-lactate dehydrogenase from Porcellio dilatatus
keywords	Gut metagenome; Oxidoreductases, Lactate dehydrogenases, OXIDOREDUCTASE; OXIDOREDUCTASE
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	54.74 Å
rg_electron	54.65 Å
i0	2116350000.00
molecular_weight	374740.0 kDa
excluded_volume	465160 Å³
envelope_volume	690120 Å³
shell_volume	104570 Å³
envelope_diameter	184.4 Å
shell_rg	57.47 Å
envelope_rg	53.66 Å
shape_rg	54.63 Å
total_rg	54.78 Å
total_atoms	26312
n_residues	3507
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	180.8 Å
rg_real	54.67 Å
rg_real_error	1.36 Å
i0_real	2.1160e+09
i0_real_error	3.8140e+07
rg_reciprocal	54.77 Å
i0_reciprocal	2117000000.0000
total_estimate	0.8209
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	68.6 Å
skewness	0.252
kurtosis	-0.481
angular_range	— – 0.1450 Å⁻¹
current_alpha	0.0002
highest_alpha	169000000.0000
n_real_points	30
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.891; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Glycolate oxidase
formula_weight	48970.3 kDa
src_method	man
entity_count	8

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F,G,H
atom_count	26348

MPGVVEELVAAIGAEQVVTDPAVMEGYSHDEAEWAPYDAPAAVVRPRDTADVAEVVRICAGRGVAVVGRGAGTGLSGAANAGRGWVVVSFERMNRVLEVDTVQQTVTVQPGVVNDDLRARVAQDGLWYPPDPASSPWSTIGGNVATNAGGLCCVKYGVTRDYVLGMEAVVGSGEVVRLGRTTAKGVTGYDLAGLMVGSEGTLGLVTEVTLRLVPLRRGVEHTVVGYFDSLTDAGRAVAAVSAAGIVPSALELIDRFCLQAVDEWKNMGLSAEGEVLLLARSDLPGTSGQEEADRILECFEKEKAVYAVRSTDEEEAEALFQARRLAYPALERLGPLLTEDVCVPKARVPHMLEAIEAAGERFDTRIGNIAHAGDGNLHPLFIVPAGDEEAKRRAKQAFEVIVDEALAVGGTVTGEHGVGLLKMRGAADELGPHVLAMHRAVKGALDPAGIFNPGKVFALEEERD

Source

organism	Porcellio dilatatus
ncbi_taxonomy_id	96809
host_organism	Escherichia coli

Entity 2 non-polymer

description	FLAVIN-ADENINE DINUCLEOTIDE
formula_weight	785.5 kDa
src_method	syn
entity_count	8

Entity 3 non-polymer

description	FE (III) ION
formula_weight	55.8 kDa
src_method	syn
entity_count	8

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	36

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6. Citations (1)

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length_a	69.668 Å
length_b	103.920 Å
length_c	143.827 Å
angle_alpha	81.94 °
angle_beta	77.24 °
angle_gamma	75.41 °
z_pdb	8

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	2.840 Å
resolution_low	78.150 Å
r_factor	0.2101
r_work	0.2074
r_free	0.2623

fit	/app/data/saxs_computation/qg/9qgz/9qgz.fit
pddf	/app/data/pr_computation/qg/9qgz/9qgz.pr.out
profile	/app/data/saxs_computation/qg/9qgz/9qgz.dat

Crystal structure of a D-lactate dehydrogenase from Porcellio dilatatus

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