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1ep3

CRYSTAL STRUCTURE OF LACTOCOCCUS LACTIS DIHYDROOROTATE DEHYDROGENASE B. DATA COLLECTED UNDER CRYOGENIC CONDITIONS.

Method: X-RAY DIFFRACTION D_max: 84.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1ep3
deposition_date	2000-03-27
title	CRYSTAL STRUCTURE OF LACTOCOCCUS LACTIS DIHYDROOROTATE DEHYDROGENASE B. DATA COLLECTED UNDER CRYOGENIC CONDITIONS.
keywords	Heterotetramer, ALPHA-BETA barrel, BETA sandwich, FAD domain, ALPHA/BETA NADP domain, FeS cluster binding domain, 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	26.31 Å
rg_electron	25.58 Å
i0	63596700.00
molecular_weight	62880.0 kDa
excluded_volume	79036 Å³
envelope_volume	92839 Å³
shell_volume	30262 Å³
envelope_diameter	89.3 Å
shell_rg	32.98 Å
envelope_rg	25.83 Å
shape_rg	25.61 Å
total_rg	26.28 Å
total_atoms	4388
n_residues	572
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	84.9 Å
rg_real	26.33 Å
rg_real_error	0.45 Å
i0_real	6.3600e+07
i0_real_error	8.2670e+05
rg_reciprocal	26.33 Å
i0_reciprocal	63600000.0000
total_estimate	0.8898
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	29.7 Å
skewness	0.414
kurtosis	-0.311
angular_range	— – 0.3000 Å⁻¹
current_alpha	0.0000
highest_alpha	18220000.0000
n_real_points	61
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.868; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.970

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	DIHYDROOROTATE DEHYDROGENASE B (PYRD SUBUNIT)
formula_weight	32977.3 kDa
ec_number	1.3.3.1
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	4854

MTENNRLSVKLPGLDLKNPIIPASGCFGFGEEYAKYYDLNKLGSIMVKATTLHPRFGNPTPRVAETASGMLNAIGLQNPGLEVIMTEKLPWLNENFPELPIIANVAGSEEADYVAVCAKIGDAANVKAIELNISCPNVKHGGQAFGTDPEVAAALVKACKAVSKVPLYVKLSPNVTDIVPIAKAVEAAGADGLTMINTLMGVRFDLKTRQPILANITGGLSGPAIKPVALKLIHQVAQDVDIPIIGMGGVANAQDVLEMYMAGASAVAVGTANFADPFVCPKIIDKLPELMDQYRIESLESLIQEVKEGKK

Source

organism	Lactococcus lactis
ncbi_taxonomy_id	1358
host_organism	Escherichia coli

Entity 2 polymer

description	DIHYDROOROTATE DEHYDROGENASE B (PYRK SUBUNIT)
formula_weight	28690.3 kDa
ec_number	1.3.3.1
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MSQLQEMMTVVSQREVAYNIFEMVLKGTLVDEMDLPGQFLHLAVPNGAMLLRRPISISSWDKRAKTCTILYRIGDETTGTYKLSKLESGAKVDVMGPLGNGFPVAEVTSTDKILIIGGGIGVPPLYELAKQLEKTGCQMTILLGFASENVKILENEFSNLKNVTLKIATDDGSYGTKGHVGMLMNEIDFEVDALYTCGAPAMLKAVAKKYDQLERLYISMESRMACGIGACYACVEHDKEDESHALKVCEDGPVFLGKQLSL

Source

organism	Lactococcus lactis
ncbi_taxonomy_id	1358
host_organism	Escherichia coli

Entity 3 non-polymer

description	FLAVIN MONONUCLEOTIDE
formula_weight	456.3 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	FLAVIN-ADENINE DINUCLEOTIDE
formula_weight	785.5 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	FE2/S2 (INORGANIC) CLUSTER
formula_weight	175.8 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	466

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6. Citations (4)

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length_a	199.890 Å
length_b	199.890 Å
length_c	80.270 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	18

space_group	H 3 2
int_tables_number	155
crystal_system	—

resolution	2.100 Å
resolution_low	20.000 Å
r_factor	—
r_work	0.1950
r_free	0.2370

fit	/app/data/saxs_computation/ep/1ep3/1ep3.fit
pddf	/app/data/pr_computation/ep/1ep3/1ep3.pr.out
profile	/app/data/saxs_computation/ep/1ep3/1ep3.dat

CRYSTAL STRUCTURE OF LACTOCOCCUS LACTIS DIHYDROOROTATE DEHYDROGENASE B. DATA COLLECTED UNDER CRYOGENIC CONDITIONS.

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

5. Entities & Polymer Info (6)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 water

6. Citations (4)

7. Files & Curves (10)

Files (7)

Curves (3)