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1e9y

Crystal structure of Helicobacter pylori urease in complex with acetohydroxamic acid

Method: X-RAY DIFFRACTION D_max: 110.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1e9y
deposition_date	2000-11-01
title	Crystal structure of Helicobacter pylori urease in complex with acetohydroxamic acid
keywords	HYDROLASE, DODECAMER; HYDROLASE
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	31.17 Å
rg_electron	30.48 Å
i0	127262000.00
molecular_weight	88390.0 kDa
excluded_volume	110190 Å³
envelope_volume	133260 Å³
shell_volume	37211 Å³
envelope_diameter	119.7 Å
shell_rg	36.70 Å
envelope_rg	30.98 Å
shape_rg	30.47 Å
total_rg	31.03 Å
total_atoms	6206
n_residues	806
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	110.9 Å
rg_real	31.26 Å
rg_real_error	0.95 Å
i0_real	1.2730e+08
i0_real_error	2.0900e+06
rg_reciprocal	31.22 Å
i0_reciprocal	127300000.0000
total_estimate	0.8567
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	34.8 Å
skewness	0.432
kurtosis	-0.209
angular_range	— – 0.2550 Å⁻¹
current_alpha	0.0000
highest_alpha	31790000.0000
n_real_points	52
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.765; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.847; Smooth: 0.990

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	UREASE SUBUNIT ALPHA
formula_weight	26571.7 kDa
ec_number	3.5.1.5
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	6272

MKLTPKELDKLMLHYAGELAKKRKEKGIKLNYVEAVALISAHIMEEARAGKKTAAELMQEGRTLLKPDDVMDGVASMIHEVGIEAMFPDGTKLVTVHTPIEANGKLVPGELFLKNEDITINEGKKAVSVKVKNVGDRPVQIGSHFHFFEVNRCLDFDREKTFGKRLDIAAGTAVRFEPGEEKSVELIDIGGNRRIFGFNALVDRQADNESKKIALHRAKERGFHGAKSDDNYVKTIKE

Source

organism	HELICOBACTER PYLORI
ncbi_taxonomy_id	210
host_organism	ESCHERICHIA COLI

Entity 2 polymer

description	UREASE SUBUNIT BETA
formula_weight	61761.4 kDa
ec_number	3.5.1.5
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MKKISRKEYVSMYGPTTGDKVRLGDTDLIAEVEHDYTIYGEELKFGGGKTLREGMSQSNNPSKEELDLIITNALIVDYTGIYKADIGIKDGKIAGIGKGGNKDMQDGVKNNLSVGPATEALAGEGLIVTAGGIDTHIHFISPQQIPTAFASGVTTMIGGGTGPADGTNATTITPGRRNLKWMLRAAEEYSMNLGFLAKGNASNDASLADQIEAGAIGFKIHEDWGTTPSAINHALDVADKYDVQVAIHTDTLNEAGCVEDTMAAIAGRTMHTFHTEGAGGGHAPDIIKVAGEHNILPASTNPTIPFTVNTEAEHMDMLMVCHHKDKSIKEDVQFADSRIRPQTIAAEDTLHDMGAFSITSSDSQAMGRVGEVITRTWQTADKNKKEFGRLKEEKGDNDNFRIKRYLSKYTINPAIAHGISEYVGSVEVGKVADLVLWSPAFFGVKPNMIIKGGFIALSQMGDANASIPTPQPVYYREMFAHHGKAKYDANITFVSQAAYDKGIKEELGLERQVLPVKNCRNVTKKDMQFNNTTAHIEVNPETYHVFVDGKEVTSKPANKVSLAQLFSIF

Source

organism	HELICOBACTER PYLORI
ncbi_taxonomy_id	210
host_organism	ESCHERICHIA COLI

Entity 3 non-polymer

description	ACETOHYDROXAMIC ACID
formula_weight	75.1 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	NICKEL (II) ION
formula_weight	58.7 kDa
src_method	syn
entity_count	2

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	66

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6. Citations (1)

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length_a	178.160 Å
length_b	178.160 Å
length_c	178.160 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	24

space_group	I 2 3
int_tables_number	197
crystal_system	—

resolution	3.000 Å
resolution_low	20.000 Å
r_factor	0.2130
r_work	0.2130
r_free	0.2820

fit	/app/data/saxs_computation/e9/1e9y/1e9y.fit
pddf	/app/data/pr_computation/e9/1e9y/1e9y.pr.out
profile	/app/data/saxs_computation/e9/1e9y/1e9y.dat

Crystal structure of Helicobacter pylori urease in complex with acetohydroxamic acid

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 (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)