SAXSdb — 9qb7

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1. Structure Basics

entry_id	9qb7
deposition_date	2025-02-28
title	Structure of rat Phospholipase C gamma 1 mutant S345F
keywords	HYDROLASE COMPLEX AUTOINHIBITED STATE, HYDROLASE, MUTANT, S345F; 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	35.63 Å
rg_electron	34.91 Å
i0	254801000.00
molecular_weight	128690.0 kDa
excluded_volume	161070 Å³
envelope_volume	214840 Å³
shell_volume	50797 Å³
envelope_diameter	117.8 Å
shell_rg	41.87 Å
envelope_rg	34.50 Å
shape_rg	34.92 Å
total_rg	35.41 Å
total_atoms	9066
n_residues	1116
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	114.5 Å
rg_real	35.51 Å
rg_real_error	0.67 Å
i0_real	2.5480e+08
i0_real_error	3.8200e+06
rg_reciprocal	35.59 Å
i0_reciprocal	254800000.0000
total_estimate	0.8911
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	46.8 Å
skewness	0.218
kurtosis	-0.386
angular_range	— – 0.2200 Å⁻¹
current_alpha	0.0001
highest_alpha	40110000.0000
n_real_points	45
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.902; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.877

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1
formula_weight	146285.0 kDa
ec_number	3.1.4.11
mutation	S345F
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	9399

MAGVGTPCANGCGPSAPSQAEVLHLCRSLEVGTVMTLFYSKKSQRPERKTFQVKLETRQITWSRGADKIEGSIDIREIKEIRPGKTSRDFDRYQEDPAFRPDQSHCFVILYGMEFRLKTLSLQATSEDEVNMWIKGLTWLMEDTLQAATPLQIERWLRKQFYSVDRNREDRISAKDLKNMLSQVNYRVPNMRFLRERLTDFEQRSGDITYGQFAQLYRSLMYSAQKTMDLPFLETNTLRTGERPELCQVSLSEFQQFLLEYQGELWAVDRLQVQEFMLSFLRDPLREIEEPYFFLDELVTFLFSKENSVWNSQLDAVCPETMNNPLSHYWISSSHNTYLTGDQFFSESSLEAYARCLRMGCRCIELDCWDGPDGMPVIYHGHTLTTKIKFSDVLHTIKEHAFVASEYPVILSIEDHCSIAQQRNMAQHFRKVLGDTLLTKPVDIAADGLPSPNQLKRKILIKHKKLAEGSAYEEVPTSVMYSENDISNSIKNGILYLEDPVNHEWYPHYFVLTSSKIYYSEETSSDQGNEDEEEPKEASGSTELHSSEKWFHGKLGAGRDGRHIAERLLTEYCIETGAPDGSFLVRESETFVGDYTLSFWRNGKVQHCRIHSRQDAGTPKFFLTDNLVFDSLYDLITHYQQVPLRCNEFEMRLSEPVPQTNAHESKEWYHASLTRAQAEHMLMRVPRDGAFLVRKRNEPNSYAISFRAEGKIKHCRVQQEGQTVMLGNSEFDSLVDLISYYEKHPLYRKMKLRYPINEEALEKIGSGSTFKCAVKALFDYKAQREDELTFTKSAIIQNVEKQDGGWWRGDYGGKKQLWFPSNYVEEMINPAILEPEREHLDENSPLGDLLRGVLDVPACQIAIRPEGKNNRLFVFSISMPSVAQWSLDVAADSQEELQDWVKKIREVAQTADARLTEGKMMERRKKIALELSELVVYCRPVPFDEEKIGTERACYRDMSSFPETKAEKYVNKAKGKKFLQYNRLQLSRIYPKGQRLDSSNYDPLPMWICGSQLVALNFQTPDKPMQMNQALFMAGGHCGYVLQPSTMRDEAFDPFDKSSLRGLEPCVICIEVLGARHLPKNGRGIVCPFVEIEVAGAEYDSTKQKTEFVVDNGLNPVWPAKPFHFQISNPEFAFLRFVVYEEDMFSDQNFLAQATFPVKGLKTGYRAVPLKNNYSEDLELASLLIKIDIFPAKENGDLSPFSGTSLRERASDASSQLFHVRAREGSFEARYQQPFEDFRISQEHLADHFDSRERRAPRRTRVNGDNRL

Source

organism	Rattus norvegicus
common_name	Norway rat
ncbi_taxonomy_id	10116
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	1

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	322

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6. Citations (1)

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length_a	72.442 Å
length_b	82.391 Å
length_c	230.676 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 21
int_tables_number	19
crystal_system	orthorhombic

resolution	2.560 Å
resolution_low	41.200 Å
r_factor	0.1904
r_work	0.1881
r_free	0.2333

fit	/app/data/saxs_computation/qb/9qb7/9qb7.fit
pddf	/app/data/pr_computation/qb/9qb7/9qb7.pr.out
profile	/app/data/saxs_computation/qb/9qb7/9qb7.dat

Structure of rat Phospholipase C gamma 1 mutant S345F

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