SAXSdb — 1dik

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1. Structure Basics

entry_id	1dik
deposition_date	1995-12-06
title	PYRUVATE PHOSPHATE DIKINASE
keywords	TRANSFERASE, KINASE, PHOSPHOTRANSFERASE; PHOSPHOTRANSFERASE
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	32.05 Å
rg_electron	31.94 Å
i0	149870000.00
molecular_weight	96327.0 kDa
excluded_volume	119920 Å³
envelope_volume	147580 Å³
shell_volume	39434 Å³
envelope_diameter	109.5 Å
shell_rg	38.13 Å
envelope_rg	31.65 Å
shape_rg	31.95 Å
total_rg	32.39 Å
total_atoms	6745
n_residues	869
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	107.4 Å
rg_real	32.18 Å
rg_real_error	0.83 Å
i0_real	1.4990e+08
i0_real_error	2.3070e+06
rg_reciprocal	32.12 Å
i0_reciprocal	149900000.0000
total_estimate	0.8724
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	35.1 Å
skewness	0.452
kurtosis	-0.347
angular_range	— – 0.2450 Å⁻¹
current_alpha	0.0000
highest_alpha	22750000.0000
n_real_points	50
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.824; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.964; Smooth: 0.900

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	PYRUVATE PHOSPHATE DIKINASE
formula_weight	96785.4 kDa
ec_number	2.7.9.1
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	7161

MAKWVYKFEEGNASMRNLLGGKGCNLAEMTILGMPIPQGFTVTTEACTEYYNSGKQITQEIQDQIFEAITWLEELNGKKFGDTEDPLLVSVRSAARASMPGMMDTILNLGLNDVAVEGFAKKTGNPRFAYDSYRRFIQMYSDVVMEVPKSHFEKIIDAMKEEKGVHFDTDLTADDLKELAEKFKAVYKEAMNGEEFPQEPKDQLMGAVKAVFRSWDNPRAIVYRRMNDIPGDWGTAVNVQTMVFGNKGETSGTGVAFTRNPSTGEKGIYGEYLINAQGEDVVAGVRTPQPITQLENDMPDCYKQFMDLAMKLEKHFRDMQDMEFTIEEGKLYFLQTRNGKRTAPAALQIACDLVDEGMITEEEAVVRIEAKSLDQLLHPTFNPAALKAGEVIGSALPASPGAAAGKVYFTADEAKAAHEKGERVILVRLETSPEDIEGMHAAEGILTVRGGMTSHAAVVARGMGTCCVSGCGEIKINEEAKTFELGGHTFAEGDYISLDGSTGKIYKGDIETQEASVSGSFERIMVWADKFRTLKVRTNADTPEDTLNAVKLGAEGIGLCRTEHMFFEADRIMKIRKMILSDSVEAREEALNELIPFQKGDFKAMYKALEGRPMTVRYLDPPLHEFVPHTEEEQAELAKNMGLTLAEVKAKVDELHEFNPMMGHRGCRLAVTYPEIAKMQTRAVMEAAIEVKEETGIDIVPEIMIPLVGEKKELKFVKDVVVEVAEQVKKEKGSDMQYHIGTMIEIPRAALTADAIAEEAEFFSFGTNDLTQMTFGFSRDDAGKFLDSYYKAKIYESDPFARLDQTGVGQLVEMAVKKGRQTRPGLKCGICGEHGGDPSSVEFCHKVGLNYVSCSPFRVPIARLAAAQAALNNK

Source

organism	Clostridium symbiosum
ncbi_taxonomy_id	1512
host_organism	Escherichia coli

Entity 2 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	3

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	416

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6. Citations (1)

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length_a	89.800 Å
length_b	58.800 Å
length_c	102.000 Å
angle_alpha	90.00 °
angle_beta	94.80 °
angle_gamma	90.00 °
z_pdb	2

space_group	P 1 2 1
int_tables_number	3
crystal_system	—

resolution	2.300 Å
resolution_low	8.000 Å
r_factor	0.1820
r_work	0.1820
r_free	—

fit	/app/data/saxs_computation/di/1dik/1dik.fit
pddf	/app/data/pr_computation/di/1dik/1dik.pr.out
profile	/app/data/saxs_computation/di/1dik/1dik.dat

PYRUVATE PHOSPHATE DIKINASE

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