SAXSdb — 1zca

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1zca
沉积日期 deposition_date	2005-04-11
结构标题 title	Crystal structure of G alpha 12 in complex with GDP, Mg2+ and AlF4-
关键词 keywords	GTP-binding, Lipoprotein, Membrane, Palmitate, Transducer, SIGNALING PROTEIN; SIGNALING PROTEIN
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	27.83 Å
回转半径 Rg (电子) rg_electron	26.86 Å
零角强度 I(0) i0	89908700.00
分子量 molecular_weight	75363.0 kDa
排除体积 excluded_volume	94927 Å³
包络体积 envelope_volume	119740 Å³
水化壳体积 shell_volume	36277 Å³
包络直径 envelope_diameter	92.7 Å
壳层 Rg shell_rg	34.93 Å
包络 Rg envelope_rg	26.87 Å
形状 Rg shape_rg	26.84 Å
总 Rg total_rg	27.77 Å
总原子数 total_atoms	5307
残基数 n_residues	635
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	87.6 Å
Rg (实空间) rg_real	27.71 Å
Rg 误差 (实空间) rg_real_error	0.46 Å
I(0) (实空间) i0_real	8.9910e+07
I(0) 误差 (实空间) i0_real_error	1.2050e+06
Rg (倒空间) rg_reciprocal	27.75 Å
I(0) (倒空间) i0_reciprocal	89910000.0000
解质量估计 total_estimate	0.9009
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	33.8 Å
偏度 Skewness skewness	0.241
峰度 Kurtosis kurtosis	-0.401
角度范围 angular_range	— – 0.2850 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	22520000.0000
实空间数据点数 n_real_points	58
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.917; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.960

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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 alpha i/12
分子量 formula_weight	41952.5 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	A,B
原子数 atom_count	5313

MGCTLSAEDKAAVERSKMIDRNLREDGERRAVRRLVKILLLGAGESGKSTFLKQMRIIHGREFDQKALLEFRDTIFDNILKGSRVLVDARDKLGIPWQHSENEKHGMFLMAFENKAGLPVEPATFQLYVPALSALWRDSGIREAFSRRSEFQLGESVKYFLDNLDRIGQLNYFPSKQDILLARKATKGIVEHDFVIKKIPFKMVDVGGQRSQRQKWFQCFDGITSILFMVSSSEYDQVLMEDRRTNRLVESMNIFETIVNNKLFFNVSIILFLNKMDLLVEKVKSVSIKKHFPDFKGDPHRLEDVQRYLVQCFDRKRRNRSKPLFHHFTTAIDTENIRFVFHAVKDTILQENLKDIMLQ

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI 分类编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Spodoptera frugiperda

Entity 2 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 3 non-polymer

描述 description	TETRAFLUOROALUMINATE ION
分子量 formula_weight	103.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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	2

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	6

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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	d1zcaa1
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	d1zcaa2
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	d1zcab1
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	d1zcab2
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

CATH v4.4 (4 domains)

结构域编号 domain_id	1zcaA01
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	1zcaA02
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	1zcaB01
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	1zcaB02
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

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7. 引用文献 (1)

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晶胞边长 a length_a	57.501 Å
晶胞边长 b length_b	85.230 Å
晶胞边长 c length_c	82.885 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	106.09 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	—

分辨率 resolution	2.900 Å
最低分辨率 resolution_low	29.100 Å
R 因子 r_factor	0.2389
R_work r_work	0.2359
R_free r_free	0.2961

fit	/app/data/saxs_computation/zc/1zca/1zca.fit
pddf	/app/data/pr_computation/zc/1zca/1zca.pr.out
profile	/app/data/saxs_computation/zc/1zca/1zca.dat

Crystal structure of G alpha 12 in complex with GDP, Mg2+ and AlF4-

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