← Back to search

1ejr

CRYSTAL STRUCTURE OF THE D221A VARIANT OF KLEBSIELLA AEROGENES UREASE

Method: X-RAY DIFFRACTION D_max: 98.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	1ejr
deposition_date	2000-03-04
title	CRYSTAL STRUCTURE OF THE D221A VARIANT OF KLEBSIELLA AEROGENES UREASE
keywords	alpha-beta barrel, nickel metalloenzyme, HYDROLASE; HYDROLASE
method	X-RAY DIFFRACTION

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	29.66 Å
rg_electron	28.74 Å
i0	107704000.00
molecular_weight	81021.0 kDa
excluded_volume	101070 Å³
envelope_volume	121800 Å³
shell_volume	35684 Å³
envelope_diameter	100.6 Å
shell_rg	35.72 Å
envelope_rg	29.01 Å
shape_rg	28.75 Å
total_rg	29.35 Å
total_atoms	5688
n_residues	753
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

▼

3. P(r) Analysis (GNOM)

dmax	98.3 Å
rg_real	29.65 Å
rg_real_error	0.74 Å
i0_real	1.0770e+08
i0_real_error	1.7330e+06
rg_reciprocal	29.66 Å
i0_reciprocal	107700000.0000
total_estimate	0.8864
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	35.3 Å
skewness	0.340
kurtosis	-0.324
angular_range	— – 0.2650 Å⁻¹
current_alpha	0.0000
highest_alpha	29720000.0000
n_real_points	54
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.880; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.890

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (5)

Entity 1 polymer

description	UREASE ALPHA SUBUNIT
formula_weight	60365.3 kDa
ec_number	3.5.1.5
mutation	D221A
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C
atom_count	6093

MSNISRQAYADMFGPTVGDKVRLADTELWIEVEDDLTTYGEEVKFGGGKVIRDGMGQGQMLAADCVDLVLTNALIVDHWGIVKADIGVKDGRIFAIGKAGNPDIQPNVTIPIGAATEVIAAEGKIVTAGGIDTHIHWICPQQAEEALVSGVTTMVGGGTGPAAGTHATTCTPGPWYISRMLQAADSLPVNIGLLGKGNVSQPDALREQVAAGVIGLKIHEAWGATPAAIDCALTVADEMDIQVALHSDTLNESGFVEDTLAAIGGRTIHTFHTEGAGGGHAPDIITACAHPNILPSSTNPTLPYTLNTIDEHLDMLMVCHHLDPDIAEDVAFAESRIRRETIAAEDVLHDLGAFSLTSSDSQAMGRVGEVILRTWQVAHRMKVQRGALAEETGDNDNFRVKRYIAKYTINPALTHGIAHEVGSIEVGKLADLVVWSPAFFGVKPATVIKGGMIAIAPMGDINASIPTPQPVHYRPMFGALGSARHHCRLTFLSQAAAANGVAERLNLRSAIAVVKGCRTVQKADMVHNSLQPNITVDAQTYEVRVDGELITSEPADVLPMAQRYFLF

Source

organism	Klebsiella aerogenes
ncbi_taxonomy_id	28451
host_organism	Escherichia coli

Entity 2 polymer

description	UREASE BETA SUBUNIT
formula_weight	11125.7 kDa
ec_number	3.5.1.5
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MIPGEYHVKPGQIALNTGRATCRVVVENHGDRPIQVGSHYHFAEVNPALKFDRQQAAGYRLNIPAGTAVRFEPGQKREVELVAFAGHRAVFGFRGEVMGPL

Source

organism	Klebsiella aerogenes
ncbi_taxonomy_id	28451
host_organism	Escherichia coli

Entity 3 polymer

description	UREASE GAMMA SUBUNIT
formula_weight	11100.9 kDa
ec_number	3.5.1.5
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A

MELTPREKDKLLLFTAALVAERRLARGLKLNYPESVALISAFIMEGARDGKSVASLMEEGRHVLTREQVMEGVPEMIPDIQVEATFPDGSKLVTVHNPII

Source

organism	Klebsiella aerogenes
ncbi_taxonomy_id	28451
host_organism	Escherichia coli

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	405

▶

6. Citations (1)

▶

length_a	170.600 Å
length_b	170.600 Å
length_c	170.600 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	24

space_group	I 21 3
int_tables_number	199
crystal_system	—

resolution	2.000 Å
resolution_low	10.000 Å
r_factor	—
r_work	0.1610
r_free	—

fit	/app/data/saxs_computation/ej/1ejr/1ejr.fit
pddf	/app/data/pr_computation/ej/1ejr/1ejr.pr.out
profile	/app/data/saxs_computation/ej/1ejr/1ejr.dat

CRYSTAL STRUCTURE OF THE D221A VARIANT OF KLEBSIELLA AEROGENES 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

5. Entities & Polymer Info (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 non-polymer

Entity 5 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)