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1c4k

ORNITHINE DECARBOXYLASE MUTANT (GLY121TYR)

Method: X-RAY DIFFRACTION D_max: 101.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1c4k
deposition_date	1999-08-26
title	ORNITHINE DECARBOXYLASE MUTANT (GLY121TYR)
keywords	DECARBOXYLASE, ORNITHINE, 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	29.95 Å
rg_electron	28.97 Å
i0	111157000.00
molecular_weight	83113.0 kDa
excluded_volume	103730 Å³
envelope_volume	130500 Å³
shell_volume	37186 Å³
envelope_diameter	107.3 Å
shell_rg	36.40 Å
envelope_rg	29.40 Å
shape_rg	28.96 Å
total_rg	29.69 Å
total_atoms	5872
n_residues	728
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	101.8 Å
rg_real	29.88 Å
rg_real_error	0.82 Å
i0_real	1.1120e+08
i0_real_error	1.6880e+06
rg_reciprocal	29.91 Å
i0_reciprocal	111200000.0000
total_estimate	0.8785
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	38.4 Å
skewness	0.276
kurtosis	-0.252
angular_range	— – 0.2650 Å⁻¹
current_alpha	0.0000
highest_alpha	22560000.0000
n_real_points	54
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.817; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.970

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	PROTEIN (ORNITHINE DECARBOXYLASE)
formula_weight	82755.8 kDa
ec_number	4.1.1.17
mutation	G121Y
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	6122

SSSLKIASTQEARQYFDTDRVVVDAVGSDFTDVGAVIAMDYETDVIDAADATKFGIPVFAVTKDAQAISADELKKIFHIIDLENKFDATVNAREIETAVNNYEDSILPPFFKSLKEYVSRYLIQFDCPGHQGGQYYRKHPAGREFYDFFGETVFRADLCNADVALGDLLIHEGPAVAAEKHAARVYNADKTYFVLGGSSNANNTVTSALVSNGDLVLFDRNNHKSVYNSALAMAGGRPVYLQTNRNPYGFIGGIYDSDFDEKKIRELAAKVDPERAKWKRPFRLAVIQLGTYDGTIYNAHEVVKRIGHLCDYIEFDSAWVGYEQFIPMMRNSSPLLIDDLGPEDPGIIVVQSVHKQQAGFSQTSQIHKKDSHIKGQLRYCDHKHFNNSFNLFMSTSPFYPMYAALDVNAAMQEGEAGRKLWHDLLITTIEARKKLIKAGSMFRPFVPPVVNGKKWEDGDTEDMANNIDYWRFEKGAKWHAYEGYGDNQYYVDPNKFMLTTPGINPETGDYEDFGVPATIVANYLRDHGIIPEKSDLNSILFLMTPAETPAKMNNLITQLLQLQRLIEEDAPLKQVLPSIYAANEERYNGYTIRELCQELHDFYKNNNTFTYQKRLFLREFFPEQGMLPYEARQEFIRNHNKLVPLNKIEGEIALEGALPYPPGVFCVAPGEKWSETAVKYFTILQDGINNFPGFAPEIQGVYFKQEGDKVVAYGEVYDAEVAKNDDRYNN

Source

organism	Lactobacillus sp. 30A
ncbi_taxonomy_id	1593
host_organism	Escherichia coli

Entity 2 non-polymer

description	PYRIDOXAL-5'-PHOSPHATE
formula_weight	247.1 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	GUANOSINE-5'-TRIPHOSPHATE
formula_weight	523.2 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	250

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6. Citations (1)

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length_a	111.800 Å
length_b	111.800 Å
length_c	135.900 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	6

space_group	P 32 2 1
int_tables_number	154
crystal_system	—

resolution	2.700 Å
resolution_low	7.000 Å
r_factor	0.2120
r_work	0.2120
r_free	0.2810

fit	/app/data/saxs_computation/c4/1c4k/1c4k.fit
pddf	/app/data/pr_computation/c4/1c4k/1c4k.pr.out
profile	/app/data/saxs_computation/c4/1c4k/1c4k.dat

ORNITHINE DECARBOXYLASE MUTANT (GLY121TYR)

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