SAXSdb — 8sod

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8sod
沉积日期 deposition_date	2023-04-28
结构标题 title	Phosphoinositide phosphate 3 kinase gamma bound with ADP and two Gbetagamma subunits in State 1
关键词 keywords	Phosphoinositide 3-Kinase, Chemotaxis, Cancer, SIGNALING PROTEIN; SIGNALING PROTEIN
实验方法 method	ELECTRON MICROSCOPY

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2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	55.85 Å
回转半径 Rg (电子) rg_electron	55.57 Å
零角强度 I(0) i0	945690000.00
分子量 molecular_weight	256810.0 kDa
排除体积 excluded_volume	321800 Å³
包络体积 envelope_volume	479400 Å³
水化壳体积 shell_volume	76170 Å³
包络直径 envelope_diameter	189.2 Å
壳层 Rg shell_rg	53.54 Å
包络 Rg envelope_rg	54.47 Å
形状 Rg shape_rg	55.52 Å
总 Rg total_rg	55.67 Å
总原子数 total_atoms	36057
残基数 n_residues	2271
球谐函数阶数 n_harmonics	20
q 范围 q_range	— – 0.5000 Å⁻¹
数据点数 n_points	101
壳层类型 shell_type	directional
溶剂电子密度 solvent_density	0.3340 e/Å³
壳层衬度 contrast_shell	0.0300 e/Å³
CRYSOL 版本 crysol_version	4.1.3

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3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	188.0 Å
Rg (实空间) rg_real	56.07 Å
Rg 误差 (实空间) rg_real_error	1.90 Å
I(0) (实空间) i0_real	9.4570e+08
I(0) 误差 (实空间) i0_real_error	2.0460e+07
Rg (倒空间) rg_reciprocal	55.65 Å
I(0) (倒空间) i0_reciprocal	945100000.0000
解质量估计 total_estimate	0.8396
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	67.1 Å
偏度 Skewness skewness	0.364
峰度 Kurtosis kurtosis	-0.476
角度范围 angular_range	— – 0.1400 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	56990000.0000
实空间数据点数 n_real_points	29
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.888; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.952; Smooth: 0.294

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4. 晶体学与实验 4. Crystallography & Experiment

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5. 实体与聚合体信息 (5)

Entity 1 polymer

描述 description	Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
分子量 formula_weight	37416.9 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	E,C
原子数 atom_count	36057

MSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

来源 Source

来源生物 organism	Bos taurus
通用名 common_name	cattle
NCBI 分类编号 ncbi_taxonomy_id	9913
宿主生物 host_organism	Spodoptera frugiperda

Entity 2 polymer

描述 description	phosphatidylinositol-4,5-bisphosphate 3-kinase
分子量 formula_weight	127573.5 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A

MHHHHHHELENYEQPVVLREDNRRRRRRMKPRSTAASLSSMELIPIEFVLPTSQRNTKTPETALLHVAGHGNVEQMKAQVWLRALETSVSADFYHRLGPDHFLLLYQKKGQWYEIYDKYQVVQTLDCLRYWKVLHRSPGQIHVVQRHAPSEETLAFQRQLNALIGYDVTDVSNVHDDELEFTRRRLVTPRMAEVAGRDPKLYAMHPWVTSKPLPEYLLKKITNNCVFIVIHRSTTSQTIKVSADDTPGTILQSFFTKMAKKKSLMDIPESQNERDFVLRVCGRDEYLVGETPIKNFQWVRQCLKNGEEIHLVLDTPPDPALDEVRKEEWPLVDDCTGVTGYHEQLTIHGKDHESVFTVSLWDCDRKFRVKIRGIDIPVLPRTADLTVFVEANIQYGQQVLCQRRTSPKPFTEEVLWNVWLEFSIKIKDLPKGALLNLQIYCGKAPALSGKTSAEMPSPESKGKAQLLYYVNLLLIDHRFLLRHGEYVLHMWQLSGKGEDQGSFNADKLTSATNPDKENSMSISILLDNYCHPIALPKHRPTPDPEGDRVRAEMPNQLRKQLEAIIATDPLNPLTAEDKELLWHFRYESLKDPKAYPKLFSSVKWGQQEIVAKTYQLLAKREVWDQSALDVGLTMQLLDCNFSDENVRAIAVQKLESLEDDDVLHYLLQLVQAVKFEPYHDSALARFLLKRGLRNKRIGHFLFWFLRSEIAQSRHYQQRFAVILEAYLRGCGTAMLHDFTQQVQVIDMLQKVTIDIKSLSAEKYDVSSQVISQLKQKLENLQNLNLPQSFRVPYDPGLKAGALVIEKCKVMASKKKPLWLEFKCADPTALSNETIGIIFKHGDDLRQDMLILQILRIMESIWETESLDLCLLPYGCISTGDKIGMIEIVKDATTIAKIQQSTVGNTGAFKDEVLSHWLKEKCPIEEKFQAAVERFVYSCAGYCVATFVLGIGDRHNDNIMISETGNLFHIDFGHILGNYKSFLGINKERVPFVLTPDFLFVMGTSGKKTSLHFQKFQDVCVKAYLALRHHTNLLIILFSMMLMTGMPQLTSKEDIEYIRDALTVGKSEEDAKKYFLDQIEVCRDKGWTVQFNWFLHLVLGIKQGEKHSA

来源 Source

来源生物 organism	Sus scrofa
通用名 common_name	pig
NCBI 分类编号 ncbi_taxonomy_id	9823
宿主生物 host_organism	Spodoptera frugiperda

Entity 3 polymer

描述 description	Phosphoinositide 3-kinase regulatory subunit 5
分子量 formula_weight	98497.8 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B

MQPGATTCTEDRIQHALERCLHGLSLSRRSTSWSAGLCLNCWSLQELVSRDPGHFLILLEQILQKTREVQEKGTYDLLAPLALLFYSTVLCTPHFPPDSDLLLKAARTYHRFLTWPVPYCSICQELLTFIDAELKAPGISYQRLVRAEQGLSTRSHRSSTVTVLLLNPVEVQAEFLDVADKLSTPGPSPHSAYITLLLHAFQATFGAHCDLSGLHRRLQSKTLAELEAIFTETAEAQELASGIGDAAEARQWLRTKLQAVGEKAGFPGVLDTAKPGKLRTIPIPVARCYTYSWNQDSFDILQEILLKEQELLQPEILDDEEDEDEEDEEEDLDADGHCAERDSVLSTGSAASHASTLSLASSQASGPTLSRQLLTSFVSGLSDGVDSGYMEDIEESAYERPRRPGGHERRGHRRPGQKFNRIYKLFKSTSQMVLRRDSRSLEGSPDSGPPLRRAGSLCSPLDSPTLPPSRAQRSRSLPQPKLSPQLPGWLLAPASRHQRRRPFLSGDEDPKASTLRVVVFGSDRISGKVARAYSNLRRLENNRPLLTRFFKLQFFYVPVKRSRGTGTPTSPAPRSQTPPLPTDAPRHPGPAELGAAPWEESTNDISHYLGMLDPWYERNVLGLMHLPPEVLCQSLKAEPRPLEGSPAQLPILADMLLYYCRFAARPVLLQVYQTELTFITGEKTTEIFIHSLELGHSAATRAIKASGPGSKRLGIDGDREAVPLTLQIIYSKGAISGRSRWSNMEKLCTSVNLSKACRQQEELDSSTEALTLNLTEVVKRQTPKSKKGFNQISTSQIKVDKVQIIGSNSCPFAVCLDQDERKILQSVIRCEVSPCYKPEKSSLCPPPQRPSYPPAPATPDLCSLLCLPIMTFSGALPGGGGSDYKDDDDK

来源 Source

来源生物 organism	Sus scrofa
通用名 common_name	pig
NCBI 分类编号 ncbi_taxonomy_id	9823
宿主生物 host_organism	Spodoptera frugiperda

Entity 4 polymer

描述 description	Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
分子量 formula_weight	8674.0 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	F,D

HHHHHHMASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPFREKKFFSAIL

来源 Source

来源生物 organism	Bos taurus
通用名 common_name	cattle
NCBI 分类编号 ncbi_taxonomy_id	9913
宿主生物 host_organism	Spodoptera frugiperda

Entity 5 non-polymer

描述 description	ADENOSINE-5'-DIPHOSPHATE
分子量 formula_weight	427.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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7. 引用文献 (1)

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晶胞边长 a length_a	1.000 Å
晶胞边长 b length_b	1.000 Å
晶胞边长 c length_c	1.000 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.00 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	—

空间群 space_group	P 1
空间群编号 int_tables_number	1
晶系 crystal_system	—

分辨率 resolution	3.40 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	167954

fit	/app/data/saxs_computation/so/8sod/8sod.fit
pddf	/app/data/pr_computation/so/8sod/8sod.pr.out
profile	/app/data/saxs_computation/so/8sod/8sod.dat

Phosphoinositide phosphate 3 kinase gamma bound with ADP and two Gbetagamma subunits in State 1

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

1. 结构基本信息 1. Structure Basics

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

4. 晶体学与实验 4. Crystallography & Experiment

晶胞参数 Unit Cell

对称性 Symmetry

冷冻电镜 EM 3D

5. 实体与聚合体信息 (5)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 polymer

聚合体 Polymer

来源 Source

Entity 4 polymer

聚合体 Polymer

来源 Source

Entity 5 non-polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)