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1djy

PHOSPHOINOSITIDE-SPECIFIC PHOSPHOLIPASE C-DELTA1 FROM RAT COMPLEXED WITH INOSITOL-2,4,5-TRISPHOSPHATE

Method: X-RAY DIFFRACTION D_max: 151.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1djy
deposition_date	1996-08-24
title	PHOSPHOINOSITIDE-SPECIFIC PHOSPHOLIPASE C-DELTA1 FROM RAT COMPLEXED WITH INOSITOL-2,4,5-TRISPHOSPHATE
keywords	PHOSPHORIC DIESTER HYDROLASE, HYDROLASE, LIPID DEGRADATION, TRANSDUCER, CALCIUM-BINDING, PHOSPHOLIPASE C, PHOSPHOINOSITIDE-SPECIFIC; LIPID DEGRADATION
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	41.54 Å
rg_electron	41.86 Å
i0	233384000.00
molecular_weight	122280.0 kDa
excluded_volume	152050 Å³
envelope_volume	198940 Å³
shell_volume	42868 Å³
envelope_diameter	158.4 Å
shell_rg	42.47 Å
envelope_rg	42.08 Å
shape_rg	41.85 Å
total_rg	41.96 Å
total_atoms	8584
n_residues	1074
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	151.2 Å
rg_real	41.99 Å
rg_real_error	1.63 Å
i0_real	2.3340e+08
i0_real_error	4.6000e+06
rg_reciprocal	41.54 Å
i0_reciprocal	233300000.0000
total_estimate	0.7997
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	35.8 Å
skewness	0.601
kurtosis	-0.193
angular_range	— – 0.1900 Å⁻¹
current_alpha	0.0003
highest_alpha	25360000.0000
n_real_points	39
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.621; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.670; Smooth: 0.859

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	PHOSPHOINOSITIDE-SPECIFIC PHOSPHOLIPASE C, ISOZYME DELTA1
formula_weight	70574.5 kDa
ec_number	3.1.4.11
mutation	DELTA(1-132) DELETION VARIANT
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	8986

GSMDQRQKLQHWIHSCLRKADKNKDNKMNFKELKDFLKELNIQVDDGYARKIFRECDHSQTDSLEDEEIETFYKMLTQRAEIDRAFEEAAGSAETLSVERLVTFLQHQQREEEAGPALALSLIERYEPSETAKAQRQMTKDGFLMYLLSADGNAFSLAHRRVYQDMDQPLSHYLVSSSHNTYLLEDQLTGPSSTEAYIRALCKGCRCLELDCWDGPNQEPIIYHGYTFTSKILFCDVLRAIRDYAFKASPYPVILSLENHCSLEQQRVMARHLRAILGPILLDQPLDGVTTSLPSPEQLKGKILLKGKKLGGLLPAGGENGSEATDVSDEVEAAEMEDEAVRSQVQHKPKEDKLKLVPELSDMIIYCKSVHFGGFSSPGTSGQAFYEMASFSESRALRLLQESGNGFVRHNVSCLSRIYPAGWRTDSSNYSPVEMWNGGCQIVALNFQTPGPEMDVYLGCFQDNGGCGYVLKPAFLRDPNTTFNSRALTQGPWWRPERLRVRIISGQQLPKVNKNKNSIVDPKVIVEIHGVGRDTGSRQTAVITNNGFNPRWDMEFEFEVTVPDLALVRFMVEDYDSSSKNDFIGQSTIPWNSLKQGYRHVHLLSKNGDQHPSATLFVKISIQD

Source

organism	Rattus norvegicus
common_name	Norway rat
ncbi_taxonomy_id	10116
host_organism	Escherichia coli

Entity 2 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	6

Entity 3 non-polymer

description	ACETATE ION
formula_weight	59.0 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	D-MYO-INOSITOL-2,4,5-TRIPHOSPHATE
formula_weight	420.1 kDa
src_method	syn
entity_count	2

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	402

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6. Citations (2)

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length_a	397.130 Å
length_b	397.130 Å
length_c	397.130 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	192

space_group	F 41 3 2
int_tables_number	210
crystal_system	—

resolution	2.800 Å
resolution_low	10.000 Å
r_factor	—
r_work	0.2100
r_free	0.2600

fit	/app/data/saxs_computation/dj/1djy/1djy.fit
pddf	/app/data/pr_computation/dj/1djy/1djy.pr.out
profile	/app/data/saxs_computation/dj/1djy/1djy.dat