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1ek0

GPPNHP-BOUND YPT51 AT 1.48 A RESOLUTION

Method: X-RAY DIFFRACTION D_max: 57.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1ek0
deposition_date	2000-03-06
title	GPPNHP-BOUND YPT51 AT 1.48 A RESOLUTION
keywords	G PROTEIN, VESICULAR TRAFFIC, GTP HYDROLYSIS, YPT/RAB PROTEIN, ENDOCYTOSIS, HYDROLASE, ENDOCYTOSIS-EXOCYTOSIS COMPLEX; ENDOCYTOSIS/EXOCYTOSIS
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	17.19 Å
rg_electron	15.60 Å
i0	7793030.00
molecular_weight	19970.0 kDa
excluded_volume	24811 Å³
envelope_volume	28019 Å³
shell_volume	15071 Å³
envelope_diameter	55.1 Å
shell_rg	21.65 Å
envelope_rg	15.94 Å
shape_rg	15.52 Å
total_rg	16.85 Å
total_atoms	1398
n_residues	168
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	57.8 Å
rg_real	17.09 Å
rg_real_error	0.26 Å
i0_real	7.7930e+06
i0_real_error	7.7830e+04
rg_reciprocal	17.10 Å
i0_reciprocal	7793000.0000
total_estimate	0.8798
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	22.8 Å
skewness	0.146
kurtosis	-0.410
angular_range	— – 0.4650 Å⁻¹
current_alpha	0.0001
highest_alpha	1357000.0000
n_real_points	77
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.812; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.999

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	PROTEIN (GTP-BINDING PROTEIN YPT51)
formula_weight	18963.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	1662

VTSIKLVLLGEAAVGKSSIVLRFVSNDFAENKEPTIGAAFLTQRVTINEHTVKFEIWDTAGQERFASLAPMYYRNAQAALVVYDVTKPQSFIKARHWVKELHEQASKDIIIALVGNKIDMLQEGGERKVAREEGEKLAEEKGLLFFETSAKTGENVNDVFLGIGEKIPLK

Source

organism	Saccharomyces cerevisiae
common_name	;baker's yeast ;
ncbi_taxonomy_id	4932
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	NICKEL (II) ION
formula_weight	58.7 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
formula_weight	522.2 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	GUANOSINE-5'-DIPHOSPHATE
formula_weight	443.2 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	209

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6. Citations (1)

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length_a	62.326 Å
length_b	62.326 Å
length_c	91.221 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	6

space_group	P 61
int_tables_number	169
crystal_system	—

resolution	1.480 Å
resolution_low	31.000 Å
r_factor	0.1780
r_work	0.1780
r_free	0.2280

fit	/app/data/saxs_computation/ek/1ek0/1ek0.fit
pddf	/app/data/pr_computation/ek/1ek0/1ek0.pr.out
profile	/app/data/saxs_computation/ek/1ek0/1ek0.dat