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1d8h

X-RAY CRYSTAL STRUCTURE OF YEAST RNA TRIPHOSPHATASE IN COMPLEX WITH SULFATE AND MANGANESE IONS.

Method: X-RAY DIFFRACTION D_max: 126.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1d8h
deposition_date	1999-10-24
title	X-RAY CRYSTAL STRUCTURE OF YEAST RNA TRIPHOSPHATASE IN COMPLEX WITH SULFATE AND MANGANESE IONS.
keywords	;RNA TRIPHOSPHATASE, BETA SUBUNIT, POLYNUCLEOTIDE 5'-TRIPHOSPHATASE, mRNA PROCESSING, mRNA CAPPING, NUCLEAR PROTEIN BETA BARREL, CATALYTIC DOMAIN, DIMER, MANGANESE-SULFATE COMPLEX, 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	36.89 Å
rg_electron	37.07 Å
i0	147967000.00
molecular_weight	98806.0 kDa
excluded_volume	124210 Å³
envelope_volume	169450 Å³
shell_volume	40524 Å³
envelope_diameter	132.6 Å
shell_rg	40.28 Å
envelope_rg	37.00 Å
shape_rg	37.08 Å
total_rg	37.23 Å
total_atoms	6957
n_residues	864
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	126.5 Å
rg_real	37.27 Å
rg_real_error	1.60 Å
i0_real	1.4800e+08
i0_real_error	3.0700e+06
rg_reciprocal	37.04 Å
i0_reciprocal	147900000.0000
total_estimate	0.8040
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	32.4 Å
skewness	0.544
kurtosis	-0.390
angular_range	— – 0.2150 Å⁻¹
current_alpha	0.0000
highest_alpha	28630000.0000
n_real_points	44
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.676; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.692; Smooth: 0.732

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	mRNA TRIPHOSPHATASE CET1
formula_weight	35691.5 kDa
ec_number	3.1.3.33
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	A,B,C
atom_count	7626

HMYRNVPIWAQKWKPTIKALQSINVKDLKIDPSFLNIIPDDDLTKSVQDWVYATIYSIAPELRSFIELEMKFGVIIDAKGPDRVNPPVSSQCVFTELDAHLTPNIDASLFKELSKYIRGISEVTENTGKFSIIESQTRDSVYRVGLSTQRPRFLRMSTDIKTGRVGQFIEKRHVAQLLLYSPKDSYDVKISLNLELPVPDNDPPEKYKSQSPISERTKDRVSYIHNDSCTRIDITKVENHNQNSKSRQSETTHEVELEINTPALLNAFDNITNDSKEYASLIRTFLNNGTIIRRKLSSLSYEIFEGSKKVM

Source

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

Entity 2 non-polymer

description	MANGANESE (II) ION
formula_weight	54.9 kDa
src_method	syn
entity_count	3

Entity 3 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	3

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	669

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6. Citations (1)

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length_a	116.436 Å
length_b	118.723 Å
length_c	85.138 Å
angle_alpha	90.00 °
angle_beta	108.06 °
angle_gamma	90.00 °
z_pdb	12

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	2.000 Å
resolution_low	25.000 Å
r_factor	—
r_work	0.2290
r_free	0.3100

fit	/app/data/saxs_computation/d8/1d8h/1d8h.fit
pddf	/app/data/pr_computation/d8/1d8h/1d8h.pr.out
profile	/app/data/saxs_computation/d8/1d8h/1d8h.dat

X-RAY CRYSTAL STRUCTURE OF YEAST RNA TRIPHOSPHATASE IN COMPLEX WITH SULFATE AND MANGANESE IONS.

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