SAXSdb — 1gp2

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1gp2
沉积日期 deposition_date	1996-11-13
结构标题 title	G PROTEIN HETEROTRIMER GI_ALPHA_1 BETA_1 GAMMA_2 WITH GDP BOUND
关键词 keywords	SIGNAL TRANSDUCTION PROTEIN, GTPASE, WD40, RAS-LIKE, COMPLEX (GTP-BINDING-TRANSDUCER), COMPLEX (GTP-BINDING-TRANSDUCER) complex; COMPLEX (GTP-BINDING/TRANSDUCER)
实验方法 method	X-RAY DIFFRACTION

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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	29.99 Å
回转半径 Rg (电子) rg_electron	29.24 Å
零角强度 I(0) i0	117133000.00
分子量 molecular_weight	82854.0 kDa
排除体积 excluded_volume	102590 Å³
包络体积 envelope_volume	130920 Å³
水化壳体积 shell_volume	37036 Å³
包络直径 envelope_diameter	99.8 Å
壳层 Rg shell_rg	36.75 Å
包络 Rg envelope_rg	29.11 Å
形状 Rg shape_rg	29.24 Å
总 Rg total_rg	29.92 Å
总原子数 total_atoms	5807
残基数 n_residues	737
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	93.7 Å
Rg (实空间) rg_real	29.92 Å
Rg 误差 (实空间) rg_real_error	0.62 Å
I(0) (实空间) i0_real	1.1710e+08
I(0) 误差 (实空间) i0_real_error	1.8480e+06
Rg (倒空间) rg_reciprocal	29.95 Å
I(0) (倒空间) i0_reciprocal	117100000.0000
解质量估计 total_estimate	0.9060
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	92.0 Å
偏度 Skewness skewness	0.233
峰度 Kurtosis kurtosis	-0.517
角度范围 angular_range	— – 0.2650 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	19440000.0000
实空间数据点数 n_real_points	54
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.953; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.914

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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	G PROTEIN GI ALPHA 1
分子量 formula_weight	40267.8 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	A
原子数 atom_count	6197

GCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDAARADDARQLFVLAGAAEEGFMTAELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMNRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYTHFTCATDTKNVQFVFDAVTDVIIKNNLKDCGLF

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	Norway rat
NCBI 分类编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Escherichia coli

Entity 2 polymer

描述 description	G PROTEIN GI BETA 1
分子量 formula_weight	37416.9 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

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

Entity 3 polymer

描述 description	G PROTEIN GI GAMMA 2
分子量 formula_weight	7845.1 kDa
突变 mutation	CHAIN G, C68S
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	G

MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPFREKKFFSAIL

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 4 non-polymer

描述 description	GUANOSINE-5'-DIPHOSPHATE
分子量 formula_weight	443.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 water

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	390

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6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1gp2a1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.66 — Transducin (alpha subunit), insertion domain
超家族 Superfamily superfamily	a.66.1 — Transducin (alpha subunit), insertion domain
家族 Family family	a.66.1.1 — Transducin (alpha subunit), insertion domain

结构域编号 domain_id	d1gp2a2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family family	c.37.1.8 — G proteins

结构域编号 domain_id	d1gp2b_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.69 — 7-bladed beta-propeller
超家族 Superfamily superfamily	b.69.4 — WD40 repeat-like
家族 Family family	b.69.4.1 — WD40-repeat

结构域编号 domain_id	d1gp2g_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.137 — Non-globular all-alpha subunits of globular proteins
超家族 Superfamily superfamily	a.137.3 — Transducin (heterotrimeric G protein), gamma chain
家族 Family family	a.137.3.1 — Transducin (heterotrimeric G protein), gamma chain

CATH v4.4 (4 domains)

结构域编号 domain_id	1gp2A01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

结构域编号 domain_id	1gp2A02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	400 — GI Alpha 1, domain 2-like
同源超家族 H-superfamily homologous superfamily	10 — GI Alpha 1, domain 2-like

结构域编号 domain_id	1gp2B00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	130 — 7 Propeller
拓扑 Topology topology	10 — Methylamine Dehydrogenase; Chain H
同源超家族 H-superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

结构域编号 domain_id	1gp2G00
类 Class class	4 — Few Secondary Structures
架构 Architecture architecture	10 — Irregular
拓扑 Topology topology	260 — G Protein Gi Gamma 2
同源超家族 H-superfamily homologous superfamily	10 — Transducin (heterotrimeric G protein), gamma chain

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7. 引用文献 (1)

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晶胞边长 a length_a	84.289 Å
晶胞边长 b length_b	84.289 Å
晶胞边长 c length_c	132.387 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	4

空间群 space_group	P 43
空间群编号 int_tables_number	78
晶系 crystal_system	—

分辨率 resolution	2.300 Å
最低分辨率 resolution_low	15.000 Å
R 因子 r_factor	0.2260
R_work r_work	0.2260
R_free r_free	0.3070

fit	/app/data/saxs_computation/gp/1gp2/1gp2.fit
pddf	/app/data/pr_computation/gp/1gp2/1gp2.pr.out
profile	/app/data/saxs_computation/gp/1gp2/1gp2.dat

G PROTEIN HETEROTRIMER GI_ALPHA_1 BETA_1 GAMMA_2 WITH GDP BOUND

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

精修参数 Refinement

衍射实验 Diffraction

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 non-polymer

Entity 5 water

6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)