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1dqx

;CRYSTAL STRUCTURE OF OROTIDINE 5'-PHOSPHATE DECARBOXYLASE COMPLEXED TO 6-HYDROXYURIDINE 5'-PHOSPHATE (BMP) ;

Method: X-RAY DIFFRACTION D_max: 148.0 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1dqx
deposition_date	2000-01-05
title	;CRYSTAL STRUCTURE OF OROTIDINE 5'-PHOSPHATE DECARBOXYLASE COMPLEXED TO 6-HYDROXYURIDINE 5'-PHOSPHATE (BMP) ;
keywords	;orotidine 5'phosphate decarboxylase, uridine 5'phosphate, UMP, OMP, 6-hydroxyuridine 5'-phosphate, BMP, TIM barrel, LYASE ;; LYASE
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	44.79 Å
rg_electron	44.76 Å
i0	207554000.00
molecular_weight	118580.0 kDa
excluded_volume	148300 Å³
envelope_volume	193840 Å³
shell_volume	35669 Å³
envelope_diameter	147.5 Å
shell_rg	50.87 Å
envelope_rg	43.15 Å
shape_rg	44.76 Å
total_rg	45.01 Å
total_atoms	8324
n_residues	1068
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	148.0 Å
rg_real	45.13 Å
rg_real_error	1.69 Å
i0_real	2.0760e+08
i0_real_error	3.6140e+06
rg_reciprocal	44.79 Å
i0_reciprocal	207500000.0000
total_estimate	0.6148
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	25.4 Å
skewness	0.243
kurtosis	-1.065
angular_range	— – 0.1750 Å⁻¹
current_alpha	0.0000
highest_alpha	29680000.0000
n_real_points	36
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.240; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.268; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	;OROTIDINE 5'-PHOSPHATE DECARBOXYLASE ;
formula_weight	29347.6 kDa
ec_number	4.1.1.23
mutation	S2H, N267D
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	8825

MHKATYKERAATHPSPVAAKLFNIMHEKQTNLCASLDVRTTKELLELVEALGPKICLLKTHVDILTDFSMEGTVKPLKALSAKYNFLLFEDRKFADIGNTVKLQYSAGVYRIAEWADITNAHGVVGPGIVSGLKQAAEEVTKEPRGLLMLAELSCKGSLSTGEYTKGTVDIAKSDKDFVIGFIAQRDMGGRDEGYDWLIMTPGVGLDDKGDALGQQYRTVDDVVSTGSDIIIVGRGLFAKGRDAKVEGERYRKAGWEAYLRRCGQQD

Source

organism	Saccharomyces cerevisiae
common_name	;baker's yeast ;
ncbi_taxonomy_id	4932
host_organism	Escherichia coli

Entity 2 non-polymer

description	6-HYDROXYURIDINE-5'-PHOSPHATE
formula_weight	340.2 kDa
src_method	syn
entity_count	4

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	501

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6. Citations (1)

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length_a	79.890 Å
length_b	79.970 Å
length_c	98.190 Å
angle_alpha	90.00 °
angle_beta	108.59 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.400 Å
resolution_low	50.000 Å
r_factor	0.2130
r_work	0.2130
r_free	0.2580

fit	/app/data/saxs_computation/dq/1dqx/1dqx.fit
pddf	/app/data/pr_computation/dq/1dqx/1dqx.pr.out
profile	/app/data/saxs_computation/dq/1dqx/1dqx.dat

;CRYSTAL STRUCTURE OF OROTIDINE 5'-PHOSPHATE DECARBOXYLASE COMPLEXED TO 6-HYDROXYURIDINE 5'-PHOSPHATE (BMP) ;

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