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117e

;THE R78K AND D117E ACTIVE SITE VARIANTS OF SACCHAROMYCES CEREVISIAE SOLUBLE INORGANIC PYROPHOSPHATASE: STRUCTURAL STUDIES AND MECHANISTIC IMPLICATIONS ;

Method: X-RAY DIFFRACTION D_max: 91.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	117e
deposition_date	1998-09-15
title	;THE R78K AND D117E ACTIVE SITE VARIANTS OF SACCHAROMYCES CEREVISIAE SOLUBLE INORGANIC PYROPHOSPHATASE: STRUCTURAL STUDIES AND MECHANISTIC IMPLICATIONS ;
keywords	ENZYME MECHANISM, IORGANIC PYROPHOSPHATASE, MUTAN STRUCTURES, 2-METAL ION MECHANISM, 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	27.29 Å
rg_electron	26.62 Å
i0	64139900.00
molecular_weight	63796.0 kDa
excluded_volume	80097 Å³
envelope_volume	92924 Å³
shell_volume	29799 Å³
envelope_diameter	94.0 Å
shell_rg	33.49 Å
envelope_rg	26.55 Å
shape_rg	26.62 Å
total_rg	27.32 Å
total_atoms	4489
n_residues	564
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	91.3 Å
rg_real	27.40 Å
rg_real_error	0.59 Å
i0_real	6.4140e+07
i0_real_error	9.5000e+05
rg_reciprocal	27.37 Å
i0_reciprocal	64140000.0000
total_estimate	0.8718
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	28.3 Å
skewness	0.445
kurtosis	-0.390
angular_range	— – 0.2900 Å⁻¹
current_alpha	0.0000
highest_alpha	18810000.0000
n_real_points	59
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.808; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.952; Smooth: 0.954

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	PROTEIN (INORGANIC PYROPHOSPHATASE)
formula_weight	32239.4 kDa
ec_number	3.6.1.1
mutation	D117E
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	4943

TYTTRQIGAKNTLEYKVYIEKDGKPVSAFHDIPLYADKENNIFNMVVEIPRWTNAKLEITKEETLNPIIQDTKKGKLRFVRNCFPHHGYIHNYGAFPQTWEDPNVSHPETKAVGDNEPIDVLEIGETIAYTGQVKQVKALGIMALLDEGETDWKVIAIDINDPLAPKLNDIEDVEKYFPGLLRATNEWFRIYKIPDGKPENQFAFSGEAKNKKYALDIIKETHDSWKQLIAGKSSDSKGIDLTNVTLPDTPTYSKAASDAIPPASLKADAPIDKSIDKWFFISGSV

Source

organism	Saccharomyces cerevisiae
common_name	;baker's yeast ;
ncbi_taxonomy_id	4932
host_organism	Escherichia coli

Entity 2 non-polymer

description	MANGANESE (II) ION
formula_weight	54.9 kDa
src_method	syn
entity_count	8

Entity 3 non-polymer

description	PHOSPHATE ION
formula_weight	95.0 kDa
src_method	syn
entity_count	3

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	454

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6. Citations (1)

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length_a	58.400 Å
length_b	102.800 Å
length_c	116.700 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	2.150 Å
resolution_low	8.000 Å
r_factor	0.1820
r_work	0.1820
r_free	0.2400

fit	/app/data/saxs_computation/17/117e/117e.fit
pddf	/app/data/pr_computation/17/117e/117e.pr.out
profile	/app/data/saxs_computation/17/117e/117e.dat

;THE R78K AND D117E ACTIVE SITE VARIANTS OF SACCHAROMYCES CEREVISIAE SOLUBLE INORGANIC PYROPHOSPHATASE: STRUCTURAL STUDIES AND MECHANISTIC IMPLICATIONS ;

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