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1e6a

Fluoride-inhibited substrate complex of Saccharomyces cerevisiae inorganic pyrophosphatase

Method: X-RAY DIFFRACTION D_max: 89.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1e6a
deposition_date	2000-08-09
title	Fluoride-inhibited substrate complex of Saccharomyces cerevisiae inorganic pyrophosphatase
keywords	PHOSPHORYL TRANSFER, HYDROLYSIS; PHOSPHORYL TRANSFER
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	27.09 Å
rg_electron	26.44 Å
i0	64982200.00
molecular_weight	64054.0 kDa
excluded_volume	80345 Å³
envelope_volume	92094 Å³
shell_volume	29659 Å³
envelope_diameter	94.7 Å
shell_rg	33.34 Å
envelope_rg	26.40 Å
shape_rg	26.44 Å
total_rg	27.13 Å
total_atoms	4504
n_residues	566
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	89.8 Å
rg_real	27.20 Å
rg_real_error	0.58 Å
i0_real	6.4980e+07
i0_real_error	8.3650e+05
rg_reciprocal	27.17 Å
i0_reciprocal	64980000.0000
total_estimate	0.8715
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	27.4 Å
skewness	0.442
kurtosis	-0.392
angular_range	— – 0.2950 Å⁻¹
current_alpha	0.0000
highest_alpha	18390000.0000
n_real_points	60
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.825; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.901; Smooth: 0.948

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	INORGANIC PYROPHOSPHATASE
formula_weight	32225.4 kDa
ec_number	3.6.1.1
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	5258

TYTTRQIGAKNTLEYKVYIEKDGKPVSAFHDIPLYADKENNIFNMVVEIPRWTNAKLEITKEETLNPIIQDTKKGKLRFVRNCFPHHGYIHNYGAFPQTWEDPNVSHPETKAVGDNDPIDVLEIGETIAYTGQVKQVKALGIMALLDEGETDWKVIAIDINDPLAPKLNDIEDVEKYFPGLLRATNEWFRIYKIPDGKPENQFAFSGEAKNKKYALDIIKETHDSWKQLIAGKSSDSKGIDLTNVTLPDTPTYSKAASDAIPPASLKADAPIDKSIDKWFFISGSV

Source

organism	SACCHAROMYCES CEREVISIAE
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	PYROPHOSPHATE 2-
formula_weight	176.0 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	FLUORIDE ION
formula_weight	19.0 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	1

Entity 6 non-polymer

description	PHOSPHATE ION
formula_weight	95.0 kDa
src_method	syn
entity_count	2

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	648

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6. Citations (1)

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length_a	57.770 Å
length_b	102.340 Å
length_c	115.630 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	1.900 Å
resolution_low	8.000 Å
r_factor	0.1550
r_work	0.1550
r_free	0.1820

fit	/app/data/saxs_computation/e6/1e6a/1e6a.fit
pddf	/app/data/pr_computation/e6/1e6a/1e6a.pr.out
profile	/app/data/saxs_computation/e6/1e6a/1e6a.dat