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1ep1

CRYSTAL STRUCTURE OF LACTOCOCCUS LACTIS DIHYDROOROTATE DEHYDROGENASE B

Method: X-RAY DIFFRACTION D_max: 87.6 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1ep1
deposition_date	2000-03-27
title	CRYSTAL STRUCTURE OF LACTOCOCCUS LACTIS DIHYDROOROTATE DEHYDROGENASE B
keywords	Heterotetramer, 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	26.52 Å
rg_electron	25.79 Å
i0	63254400.00
molecular_weight	62648.0 kDa
excluded_volume	78754 Å³
envelope_volume	93911 Å³
shell_volume	30424 Å³
envelope_diameter	93.3 Å
shell_rg	33.10 Å
envelope_rg	26.03 Å
shape_rg	25.82 Å
total_rg	26.49 Å
total_atoms	4373
n_residues	570
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	87.6 Å
rg_real	26.56 Å
rg_real_error	0.43 Å
i0_real	6.3250e+07
i0_real_error	8.7390e+05
rg_reciprocal	26.55 Å
i0_reciprocal	63250000.0000
total_estimate	0.6854
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	29.2 Å
skewness	0.423
kurtosis	-0.295
angular_range	— – 0.3000 Å⁻¹
current_alpha	0.0001
highest_alpha	20840000.0000
n_real_points	61
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.832; Stabil: 1.000; Sysdev: 0.145; Positv: 1.000; Valcen: 0.976; Smooth: 0.997

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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	4568

MTENNRLSVKLPGLDLKNPIIPASGCFGFGEEYAKYYDLNKLGSIMVKATTLHPRFGNPTPRVAETASGMLNAIGLQNPGLEVIMTEKLPWLNENFPELPIIANVAGSEEADYVAVCAKIGDAANVKAIELNISCPNVKHGGQAFGTDPEVAAALVKACKAVSKVPLYVKLSPNVTDIVPIAKAVEAAGADGLTMINTLMGVRFDLKTRQPILANITGGLSGPAIKPVALKLIHQVAQDVDIPIIGMGGVANAQDVLEMYMAGASAVAVGTANFADPFVCPKIIDKLPELMDQYRIESLESLIQEVKEGKK

Source

organism	Lactococcus lactis
ncbi_taxonomy_id	1358
host_organism	Escherichia coli

Entity 2 polymer

description	DIHYDROOROTATE DEHYDROGENASE B (PYRK SUBUNIT)
formula_weight	28559.1 kDa
ec_number	1.3.3.1
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

SQLQEMMTVVSQREVAYNIFEMVLKGTLVDEMDLPGQFLHLAVPNGAMLLRRPISISSWDKRAKTCTILYRIGDETTGTYKLSKLESGAKVDVMGPLGNGFPVAEVTSTDKILIIGGGIGVPPLYELAKQLEKTGCQMTILLGFASENVKILENEFSNLKNVTLKIATDDGSYGTKGHVGMLMNEIDFEVDALYTCGAPAMLKAVAKKYDQLERLYISMESRMACGIGACYACVEHDKEDESHALKVCEDGPVFLGKQLSL

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	195

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6. Citations (1)

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length_a	202.670 Å
length_b	202.670 Å
length_c	81.110 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	2.200 Å
resolution_low	30.700 Å
r_factor	—
r_work	0.2020
r_free	0.2560

fit	/app/data/saxs_computation/ep/1ep1/1ep1.fit
pddf	/app/data/pr_computation/ep/1ep1/1ep1.pr.out
profile	/app/data/saxs_computation/ep/1ep1/1ep1.dat

CRYSTAL STRUCTURE OF LACTOCOCCUS LACTIS DIHYDROOROTATE DEHYDROGENASE B

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 (1)

7. Files & Curves (10)

Files (7)

Curves (3)