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9qit

Crystal structure of a D-lactate dehydrogenase in complex with D-lactate from Porcellio dilatatus

Method: X-RAY DIFFRACTION D_max: 175.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qit
deposition_date	2025-03-17
title	Crystal structure of a D-lactate dehydrogenase in complex with D-lactate 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	52.23 Å
rg_electron	51.97 Å
i0	2241650000.00
molecular_weight	385760.0 kDa
excluded_volume	478680 Å³
envelope_volume	649970 Å³
shell_volume	101920 Å³
envelope_diameter	182.6 Å
shell_rg	57.57 Å
envelope_rg	50.69 Å
shape_rg	51.98 Å
total_rg	52.08 Å
total_atoms	27170
n_residues	3599
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	175.0 Å
rg_real	52.13 Å
rg_real_error	1.59 Å
i0_real	2.2420e+09
i0_real_error	4.4000e+07
rg_reciprocal	52.30 Å
i0_reciprocal	2242000000.0000
total_estimate	0.8807
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	64.2 Å
skewness	0.228
kurtosis	-0.407
angular_range	— – 0.1500 Å⁻¹
current_alpha	0.0001
highest_alpha	170700000.0000
n_real_points	31
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.876; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.831

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

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	27170

MPGVVEELVAAIGAEQVVTDPAVMEGYSHDEAEWAPYDAPAAVVRPRDTADVAEVVRICAGRGVAVVGRGAGTGLSGAANAGRGWVVVSFERMNRVLEVDTVQQTVTVQPGVVNDDLRARVAQDGLWYPPDPASSPWSTIGGNVATNAGGLCCVKYGVTRDYVLGMEAVVGSGEVVRLGRTTAKGVTGYDLAGLMVGSEGTLGLVTEVTLRLVPLRRGVEHTVVGYFDSLTDAGRAVAAVSAAGIVPSALELIDRFCLQAVDEWKNMGLSAEGEVLLLARSDLPGTSGQEEADRILECFEKEKAVYAVRSTDEEEAEALFQARRLAYPALERLGPLLTEDVCVPKARVPHMLEAIEAAGERFDTRIGNIAHAGDGNLHPLFIVPAGDEEAKRRAKQAFEVIVDEALAVGGTVTGEHGVGLLKMRGAADELGPHVLAMHRAVKGALDPAGIFNPGKVFALEEERD

Source

organism	Porcellio dilatatus
ncbi_taxonomy_id	96809
host_organism	Escherichia coli

Entity 2 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	4

Entity 3 non-polymer

description	LACTIC ACID
formula_weight	90.1 kDa
src_method	syn
entity_count	8

Entity 4 non-polymer

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

Entity 5 non-polymer

description	FE (III) ION
formula_weight	55.8 kDa
src_method	syn
entity_count	5

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6. Citations (1)

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length_a	127.225 Å
length_b	109.644 Å
length_c	143.437 Å
angle_alpha	90.00 °
angle_beta	98.26 °
angle_gamma	90.00 °
z_pdb	16

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	3.040 Å
resolution_low	88.110 Å
r_factor	0.2095
r_work	0.2067
r_free	0.2633

fit	/app/data/saxs_computation/qi/9qit/9qit.fit
pddf	/app/data/pr_computation/qi/9qit/9qit.pr.out
profile	/app/data/saxs_computation/qi/9qit/9qit.dat