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1e9z

Crystal structure of Helicobacter pylori urease

Method: X-RAY DIFFRACTION D_max: 110.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1e9z
deposition_date	2000-11-01
title	Crystal structure of Helicobacter pylori urease
keywords	HYDROLASE; 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	31.08 Å
rg_electron	30.39 Å
i0	126883000.00
molecular_weight	88299.0 kDa
excluded_volume	110100 Å³
envelope_volume	132130 Å³
shell_volume	37014 Å³
envelope_diameter	120.5 Å
shell_rg	36.59 Å
envelope_rg	30.85 Å
shape_rg	30.39 Å
total_rg	30.93 Å
total_atoms	6200
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	110.4 Å
rg_real	31.17 Å
rg_real_error	0.99 Å
i0_real	1.2690e+08
i0_real_error	2.0320e+06
rg_reciprocal	31.14 Å
i0_reciprocal	126900000.0000
total_estimate	0.8547
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	34.6 Å
skewness	0.428
kurtosis	-0.225
angular_range	— – 0.2550 Å⁻¹
current_alpha	0.0000
highest_alpha	30230000.0000
n_real_points	52
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.769; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.849; Smooth: 0.950

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

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	6278

MKLTPKELDKLMLHYAGELAKKRKEKGIKLNYVEAVALISAHIMEEARAGKKTAAELMQEGRTLLKPDDVMDGVASMIHEVGIEAMFPDGTKLVTVHTPIEANGKLVPGELFLKNEDITINEGKKAVSVKVKNVGDRPVQIGSHFHFFEVNRCLDFDREKTFGKRLDIAAGTAVRFEPGEEKSVELIDIGGNRRIFGFNALVDRQADNESKKIALHRAKERGFHGAKSDDNYVKTIKE

Source

organism	HELICOBACTER PYLORI
ncbi_taxonomy_id	210
host_organism	ESCHERICHIA COLI

Entity 2 polymer

description	UREASE SUBUNIT BETA
formula_weight	61745.4 kDa
ec_number	3.5.1.5
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MKKISRKEYVSMYGPTTGDKVRLGDTDLIAEVEHDYTIYGEELKFGGGKTLREGMSQSNNPSKEELDLIITNALIVDYTGIYKADIGIKDGKIAGIGKGGNKDMQDGVKNNLSVGPATEALAGEGLIVTAGGIDTHIHFISPQQIPTAFASGVTTMIGGGTGPADGTNATTITPGRRNLKWMLRAAEEYSMNLGFLAKGNASNDASLADQIEAGAIGFKIHEDWGTTPSAINHALDVADKYDVQVAIHTDTLNEAGCVEDTMAAIAGRTMHTFHTEGAGGGHAPDIIKVAGEHNILPASTNPTIPFTVNTEAEHMDMLMVCHHLDKSIKEDVQFADSRIRPQTIAAEDTLHDMGAFSITSSDSQAMGRVGEVITRTWQTADKNKKEFGRLKEEKGDNDNFRIKRYLSKYTINPAIAHGISEYVGSVEVGKVADLVLWSPAFFGVKPNMIIKGGFIALSQMGDANASIPTPQPVYYREMFAHHGKAKYDANITFVSQAAYDKGIKEELGLERQVLPVKNCRNVTKKDMQFNNTTAHIEVNPETYHVFVDGKEVTSKPANKVSLAQLFSIF

Source

organism	HELICOBACTER PYLORI
ncbi_taxonomy_id	210
host_organism	ESCHERICHIA COLI

Entity 3 non-polymer

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

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	78

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6. Citations (1)

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length_a	177.910 Å
length_b	177.910 Å
length_c	177.910 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	0.2120
r_work	0.2120
r_free	0.2840

fit	/app/data/saxs_computation/e9/1e9z/1e9z.fit
pddf	/app/data/pr_computation/e9/1e9z/1e9z.pr.out
profile	/app/data/saxs_computation/e9/1e9z/1e9z.dat

Crystal structure of Helicobacter pylori urease

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 (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)