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9rc7

Crystal structure of Gilliamella bombicola lactate deydrogenase (GbLDH)

Method: X-RAY DIFFRACTION D_max: 209.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9rc7
deposition_date	2025-05-27
last_revision	2026-04-08
title	Crystal structure of Gilliamella bombicola lactate deydrogenase (GbLDH)
keywords	dehydrogenase, 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	68.58 Å
rg_electron	68.43 Å
i0	5501910000.00
molecular_weight	631900.0 kDa
excluded_volume	792960 Å³
envelope_volume	1133400 Å³
shell_volume	138300 Å³
envelope_diameter	241.7 Å
shell_rg	67.41 Å
envelope_rg	66.56 Å
shape_rg	68.43 Å
total_rg	68.38 Å
total_atoms	44496
n_residues	5840
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	209.4 Å
rg_real	68.72 Å
rg_real_error	1.43 Å
i0_real	5.5010e+09
i0_real_error	1.1620e+08
rg_reciprocal	67.86 Å
i0_reciprocal	5492000000.0000
total_estimate	0.8122
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	63.7 Å
skewness	0.411
kurtosis	-0.580
angular_range	— – 0.1150 Å⁻¹
current_alpha	0.0003
highest_alpha	1080000000.0000
n_real_points	24
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.851; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.004

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	L-lactate oxidase
formula_weight	39086.3 kDa
src_method	man
entity_count	16

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P
atom_count	44918

MSYHTSNEEHAIEIVNIASLEALVKARMEAGAFGYIRGGAEDEWTMRENTLSFNRKKIIPRVLQGIDHADLSTKLWDIPLKTPIIQAPSAAQGLAHEQGEKDTAKGVAAAGSIFCISTYANTSIEDAANAAPNVPYFFQLYMSKDDDFNRFIIDKAVKAGTKAIILTVDSTLGGYREEDIVNKFQFPLPMKNLSAYSQSNGNGDGSGKGISEIYAAAKQGIVPSDIQKIKDMANLPVIVKGIQSPEDASIAISAGADGIWISNHGGRQLDGAPASFEVLPSIAATVAKRVPIIFDSGVRRGEHVFKALASGADLVAIGRPILYGLNLGGAEGVKSVFDHLNKELSITMQLAGTKTIEDIKNTLLI

Source

organism	Gilliamella bombicola
ncbi_taxonomy_id	1798182
host_organism	Escherichia coli

Entity 2 non-polymer

description	FLAVIN MONONUCLEOTIDE
formula_weight	456.3 kDa
src_method	syn
entity_count	16

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	422

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6. Citations (1)

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length_a	93.229 Å
length_b	93.559 Å
length_c	192.842 Å
angle_alpha	100.42 °
angle_beta	91.82 °
angle_gamma	90.19 °
z_pdb	16

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	2.200 Å
resolution_low	49.240 Å
r_factor	0.2309
r_work	0.2300
r_free	0.2478

fit	/app/data/saxs_computation/rc/9rc7/9rc7.fit
pddf	/app/data/pr_computation/rc/9rc7/9rc7.pr.out
profile	/app/data/saxs_computation/rc/9rc7/9rc7.dat

Crystal structure of Gilliamella bombicola lactate deydrogenase (GbLDH)

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