SAXSdb — 2gvz

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2gvz
沉积日期 deposition_date	2006-05-03
结构标题 title	Crystal Structure of Complex of Gs- with The Catalytic Domains of Mammalian Adenylyl Cyclase: Complex with MANT-ATP and Mn
关键词 keywords	ADENYLYL CYCLASE, MANT-ATP, LYASE; LYASE
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	31.73 Å
回转半径 Rg (电子) rg_electron	31.10 Å
零角强度 I(0) i0	110055000.00
分子量 molecular_weight	82168.0 kDa
排除体积 excluded_volume	102290 Å³
包络体积 envelope_volume	127960 Å³
水化壳体积 shell_volume	34304 Å³
包络直径 envelope_diameter	104.4 Å
壳层 Rg shell_rg	37.91 Å
包络 Rg envelope_rg	31.02 Å
形状 Rg shape_rg	31.09 Å
总 Rg total_rg	31.68 Å
总原子数 total_atoms	5751
残基数 n_residues	707
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	101.4 Å
Rg (实空间) rg_real	31.75 Å
Rg 误差 (实空间) rg_real_error	0.72 Å
I(0) (实空间) i0_real	1.1010e+08
I(0) 误差 (实空间) i0_real_error	1.8380e+06
Rg (倒空间) rg_reciprocal	31.75 Å
I(0) (倒空间) i0_reciprocal	110100000.0000
解质量估计 total_estimate	0.8969
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	30.4 Å
偏度 Skewness skewness	0.258
峰度 Kurtosis kurtosis	-0.700
角度范围 angular_range	— – 0.2500 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	26440000.0000
实空间数据点数 n_real_points	51
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.922; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.969; Smooth: 0.920

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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 (8)

Entity 1 polymer

描述 description	Adenylate cyclase type 5
分子量 formula_weight	25526.5 kDa
EC 编号 ec_number	4.6.1.1
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	5751

MHHHHHHAMEMKADINAKQEDMMFHKIYIQKHDNVSILFADIEGFTSLASQCTAQELVMTLNELFARFDKLAAENHCLRIKILGDCYYCVSGLPEARADHAHCCVEMGMDMIEAISLVREMTGVNVNMRVGIHSGRVHCGVLGLRKWQFDVWSNDVTLANHMEAGGKAGRIHITKATLSYLNGDYEVEPGCGGERNAYLKEHSIETFLILRCTQKRKEEKAMIAK

来源 Source

来源生物 organism	Canis lupus familiaris
通用名 common_name	dog
NCBI 分类编号 ncbi_taxonomy_id	9615
宿主生物 host_organism	Escherichia coli BL21

Entity 2 polymer

描述 description	Adenylate cyclase type 2
分子量 formula_weight	23717.0 kDa
EC 编号 ec_number	4.6.1.1
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

RSLKNEELYHQSYDCVCVMFASIPDFKEFYTESDVNKEGLECLRLLNEIIADFDDLLSKPKFSGVEKIKTIGSTYMAATGLSAIPSQEHAQEPERQYMHIGTMVEFAYALVGKLDAINKHSFNDFKLRVGINHGPVIAGVIGAQKPQYDIWGNTVNVASRMDSTGVLDKIQVTEETSLILQTLGYTCTCRGIINVKGKGDLKTYFVNTEMSR

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 BL21

Entity 3 polymer

描述 description	Guanine nucleotide-binding protein G(s), alpha subunit
分子量 formula_weight	45769.5 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	C

MGCLGNSKTEDQRNEEKAQREANKKIEKQLQKDKQVYRATHRLLLLGAGESGKSTIVKQMRILHVNGFNGEGGEEDPQAARSNSDGEKATKVQDIKNNLKEAIETIVAAMSNLVPPVELANPENQFRVDYILSVMNVPDFDFPPEFYEHAKALWEDEGVRACYERSNEYQLIDCAQYFLDKIDVIKQDDYVPSDQDLLRCRVLTSGIFETKFQVDKVNFHMFDVGGQRDERRKWIQCFNDVTAIIFVVASSSYNMVIREDNQTNRLQEALNLFKSIWNNRWLRTISVILFLNKQDLLAEKVLAGKSKIEDYFPEFARYTTPEDATPEPGEDPRVTRAKYFIRDEFLRISTASGDGRHYCYPHFTCAVDTENIRRVFNDCRDIIQRMHLRQYELL

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	Escherichia coli BL21

Entity 4 non-polymer

描述 description	MANGANESE (II) ION
分子量 formula_weight	54.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 5 non-polymer

描述 description	METHYLPIPERAZINOFORSKOLIN
分子量 formula_weight	550.7 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 6 non-polymer

描述 description	;3'-O-[2-(METHYLAMINO)BENZOYL]ADENOSINE 5'-(TETRAHYDROGEN TRIPHOSPHATE) ;
分子量 formula_weight	640.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 7 non-polymer

描述 description	CHLORIDE ION
分子量 formula_weight	35.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 8 non-polymer

描述 description	5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE
分子量 formula_weight	539.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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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	d2gvza1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.58 — Ferredoxin-like
超家族 Superfamily superfamily	d.58.29 — Nucleotide cyclase
家族 Family family	d.58.29.1 — Adenylyl and guanylyl cyclase catalytic domain

结构域编号 domain_id	d2gvzb1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.58 — Ferredoxin-like
超家族 Superfamily superfamily	d.58.29 — Nucleotide cyclase
家族 Family family	d.58.29.1 — Adenylyl and guanylyl cyclase catalytic domain

结构域编号 domain_id	d2gvzc1
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	d2gvzc2
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	2gvzA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	1230 — Nucleotide cyclase, GGDEF domain

结构域编号 domain_id	2gvzB00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	1230 — Nucleotide cyclase, GGDEF domain

结构域编号 domain_id	2gvzC01
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	2gvzC02
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	116.800 Å
晶胞边长 b length_b	132.100 Å
晶胞边长 c length_c	69.600 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 21 21 2
空间群编号 int_tables_number	18
晶系 crystal_system	—

分辨率 resolution	3.270 Å
最低分辨率 resolution_low	14.970 Å
R 因子 r_factor	0.2750
R_work r_work	0.2750
R_free r_free	0.3300

fit	/app/data/saxs_computation/gv/2gvz/2gvz.fit
pddf	/app/data/pr_computation/gv/2gvz/2gvz.pr.out
profile	/app/data/saxs_computation/gv/2gvz/2gvz.dat

Crystal Structure of Complex of Gs- with The Catalytic Domains of Mammalian Adenylyl Cyclase: Complex with MANT-ATP and Mn

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 (8)

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 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 non-polymer

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)