1s7g

Structural Basis for the Mechanism and Regulation of Sir2 Enzymes

Method: X-RAY DIFFRACTION D_max: 113.2 Å Quality: EXCELLENT

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

下载 Download SAXS (.dat) P(r) (.pr.out) CIF

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1s7g
沉积日期 deposition_date	2004-01-29
结构标题 title	Structural Basis for the Mechanism and Regulation of Sir2 Enzymes
关键词 keywords	enzyme, sirtuin, sir2, NAD+, ADP-ribose, TRANSCRIPTION; TRANSCRIPTION
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	36.21 Å
回转半径 Rg (电子) rg_electron	35.68 Å
零角强度 I(0) i0	314115000.00
分子量 molecular_weight	141440.0 kDa
排除体积 excluded_volume	176120 Å³
包络体积 envelope_volume	229740 Å³
水化壳体积 shell_volume	53848 Å³
包络直径 envelope_diameter	119.8 Å
壳层 Rg shell_rg	42.08 Å
包络 Rg envelope_rg	35.15 Å
形状 Rg shape_rg	35.67 Å
总 Rg total_rg	36.13 Å
总原子数 total_atoms	9874
残基数 n_residues	1244
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	113.2 Å
Rg (实空间) rg_real	36.06 Å
Rg 误差 (实空间) rg_real_error	0.78 Å
I(0) (实空间) i0_real	3.1410e+08
I(0) 误差 (实空间) i0_real_error	4.9360e+06
Rg (倒空间) rg_reciprocal	36.16 Å
I(0) (倒空间) i0_reciprocal	314100000.0000
解质量估计 total_estimate	0.9043
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	46.3 Å
偏度 Skewness skewness	0.175
峰度 Kurtosis kurtosis	-0.511
角度范围 angular_range	— – 0.2200 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	41330000.0000
实空间数据点数 n_real_points	45
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.937; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.947

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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 (11)

Entity 1 polymer

描述 description	NAD-dependent deacetylase 2
分子量 formula_weight	28537.0 kDa
EC 编号 ec_number	3.5.1.-
来源方法 src_method	man
拷贝数 entity_count	5

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E
原子数 atom_count	10187

MEDEIRKAAEILAKSKHAVVFTGAGISAESGIPTFRGEDGLWRKYDPEEVASISGFKRNPRAFWEFSMEMKDKLFAEPNPAHYAIAELERMGIVKAVITQNIDMLHQRAGSRRVLELHGSMDKLDCLDCHETYDWSEFVEDFNKGEIPRCRKCGSYYVKPRVVLFGEPLPQRTLFEAIEEAKHCDAFMVVGSSLVVYPAAELPYIAKKAGAKMIIVNAEPTMADPIFDVKIIGKAGEVLPKIVEEVKRLRSEK

来源 Source

来源生物 organism	Archaeoglobus fulgidus
NCBI 分类编号 ncbi_taxonomy_id	2234
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	9

Entity 3 non-polymer

描述 description	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	12

Entity 4 non-polymer

描述 description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
分子量 formula_weight	663.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 5 non-polymer

描述 description	PENTAETHYLENE GLYCOL
分子量 formula_weight	238.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 6 non-polymer

描述 description	1,2-ETHANEDIOL
分子量 formula_weight	62.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 7 non-polymer

描述 description	NONAETHYLENE GLYCOL
分子量 formula_weight	414.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 8 non-polymer

描述 description	HEXAETHYLENE GLYCOL
分子量 formula_weight	282.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 9 non-polymer

描述 description	TETRAETHYLENE GLYCOL
分子量 formula_weight	194.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 10 non-polymer

描述 description	ADENOSINE-5-DIPHOSPHORIBOSE
分子量 formula_weight	559.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 11 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	313

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6. 折叠分类 (SCOP + CATH) 15 domains

SCOP 2.08 (5 domains)

结构域编号 domain_id	d1s7ga_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.31 — DHS-like NAD/FAD-binding domain
超家族 Superfamily superfamily	c.31.1 — DHS-like NAD/FAD-binding domain
家族 Family family	c.31.1.5 — Sir2 family of transcriptional regulators

结构域编号 domain_id	d1s7gb_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.31 — DHS-like NAD/FAD-binding domain
超家族 Superfamily superfamily	c.31.1 — DHS-like NAD/FAD-binding domain
家族 Family family	c.31.1.5 — Sir2 family of transcriptional regulators

结构域编号 domain_id	d1s7gc_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.31 — DHS-like NAD/FAD-binding domain
超家族 Superfamily superfamily	c.31.1 — DHS-like NAD/FAD-binding domain
家族 Family family	c.31.1.5 — Sir2 family of transcriptional regulators

结构域编号 domain_id	d1s7gd_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.31 — DHS-like NAD/FAD-binding domain
超家族 Superfamily superfamily	c.31.1 — DHS-like NAD/FAD-binding domain
家族 Family family	c.31.1.5 — Sir2 family of transcriptional regulators

结构域编号 domain_id	d1s7ge_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.31 — DHS-like NAD/FAD-binding domain
超家族 Superfamily superfamily	c.31.1 — DHS-like NAD/FAD-binding domain
家族 Family family	c.31.1.5 — Sir2 family of transcriptional regulators

CATH v4.4 (10 domains)

结构域编号 domain_id	1s7gA01
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	1220 — TPP-binding domain

结构域编号 domain_id	1s7gA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1600 — SIR2/SIRT2 'Small Domain'
同源超家族 H-superfamily homologous superfamily	10 — SIR2/SIRT2 'Small Domain'

结构域编号 domain_id	1s7gB01
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	1220 — TPP-binding domain

结构域编号 domain_id	1s7gB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1600 — SIR2/SIRT2 'Small Domain'
同源超家族 H-superfamily homologous superfamily	10 — SIR2/SIRT2 'Small Domain'

结构域编号 domain_id	1s7gC01
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	1220 — TPP-binding domain

结构域编号 domain_id	1s7gC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1600 — SIR2/SIRT2 'Small Domain'
同源超家族 H-superfamily homologous superfamily	10 — SIR2/SIRT2 'Small Domain'

结构域编号 domain_id	1s7gD01
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	1220 — TPP-binding domain

结构域编号 domain_id	1s7gD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1600 — SIR2/SIRT2 'Small Domain'
同源超家族 H-superfamily homologous superfamily	10 — SIR2/SIRT2 'Small Domain'

结构域编号 domain_id	1s7gE01
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	1220 — TPP-binding domain

结构域编号 domain_id	1s7gE02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1600 — SIR2/SIRT2 'Small Domain'
同源超家族 H-superfamily homologous superfamily	10 — SIR2/SIRT2 'Small Domain'

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7. 引用文献 (1)

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晶胞边长 a length_a	104.850 Å
晶胞边长 b length_b	181.574 Å
晶胞边长 c length_c	78.921 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	20

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	2.300 Å
最低分辨率 resolution_low	29.780 Å
R 因子 r_factor	0.2070
R_work r_work	0.2070
R_free r_free	0.2490

fit	/app/data/saxs_computation/s7/1s7g/1s7g.fit
pddf	/app/data/pr_computation/s7/1s7g/1s7g.pr.out
profile	/app/data/saxs_computation/s7/1s7g/1s7g.dat