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1dvj

CRYSTAL STRUCTURE OF OROTIDINE MONOPHOSPHATE DECARBOXYLASE COMPLEXED WITH 6-AZAUMP

Method: X-RAY DIFFRACTION D_max: 142.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1dvj
deposition_date	2000-03-30
title	CRYSTAL STRUCTURE OF OROTIDINE MONOPHOSPHATE DECARBOXYLASE COMPLEXED WITH 6-AZAUMP
keywords	TIM barrel, dimer, 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	43.66 Å
rg_electron	43.53 Å
i0	151345000.00
molecular_weight	98482.0 kDa
excluded_volume	122650 Å³
envelope_volume	176230 Å³
shell_volume	36487 Å³
envelope_diameter	139.7 Å
shell_rg	44.95 Å
envelope_rg	41.82 Å
shape_rg	43.52 Å
total_rg	43.61 Å
total_atoms	6893
n_residues	900
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	142.3 Å
rg_real	43.72 Å
rg_real_error	1.62 Å
i0_real	1.5130e+08
i0_real_error	2.7610e+06
rg_reciprocal	43.66 Å
i0_reciprocal	151300000.0000
total_estimate	0.7767
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	59.3 Å
skewness	0.134
kurtosis	-0.821
angular_range	— – 0.1800 Å⁻¹
current_alpha	0.0000
highest_alpha	6524000.0000
n_real_points	37
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.759; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.818; 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	26664.6 kDa
ec_number	4.1.1.23
mutation	R101P, EXTRA C-TERMINAL RESIDUES FROM THE CLONING VECTOR: EDPAANKARKEAELAAATA
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	7675

RSRRVDVMDVMNRLILAMDLMNRDDALRVTGEVREYIDTVKIGYPLVLSEGMDIIAEFRKRFGCRIIADFKVADIPETNEKICRATFKAGADAIIVHGFPGADSVRACLNVAEEMGREVFLLTEMSHPGAEMFIQGAADEIARMGVDLGVKNYVGPSTRPERLSRLREIIGQDSFLISPGVGAQGGDPGETLRFADAIIVGRSIYLADNPAAAAAGIIESIKDLLIPEDPAANKARKEAELAAATA

Source

organism	Methanothermobacter thermautotrophicus
ncbi_taxonomy_id	145262
host_organism	Escherichia coli

Entity 2 non-polymer

description	;6-AZA URIDINE 5'-MONOPHOSPHATE ;
formula_weight	325.2 kDa
src_method	syn
entity_count	4

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	702

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6. Citations (1)

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length_a	72.950 Å
length_b	98.620 Å
length_c	73.250 Å
angle_alpha	90.00 °
angle_beta	104.03 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.500 Å
resolution_low	30.000 Å
r_factor	0.1740
r_work	0.1740
r_free	0.1880

fit	/app/data/saxs_computation/dv/1dvj/1dvj.fit
pddf	/app/data/pr_computation/dv/1dvj/1dvj.pr.out
profile	/app/data/saxs_computation/dv/1dvj/1dvj.dat

CRYSTAL STRUCTURE OF OROTIDINE MONOPHOSPHATE DECARBOXYLASE COMPLEXED WITH 6-AZAUMP

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