2gk6

Structural and Functional insights into the human Upf1 helicase core

Method: X-RAY DIFFRACTION D_max: 122.3 Å Quality: GOOD

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	2gk6
沉积日期 deposition_date	2006-03-31
结构标题 title	Structural and Functional insights into the human Upf1 helicase core
关键词 keywords	Upf1, helicase, NMD, HYDROLASE; HYDROLASE
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	36.81 Å
回转半径 Rg (电子) rg_electron	36.52 Å
零角强度 I(0) i0	278617000.00
分子量 molecular_weight	136100.0 kDa
排除体积 excluded_volume	171110 Å³
包络体积 envelope_volume	231070 Å³
水化壳体积 shell_volume	52717 Å³
包络直径 envelope_diameter	129.2 Å
壳层 Rg shell_rg	42.85 Å
包络 Rg envelope_rg	36.13 Å
形状 Rg shape_rg	36.51 Å
总 Rg total_rg	36.97 Å
总原子数 total_atoms	9562
残基数 n_residues	1204
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	122.3 Å
Rg (实空间) rg_real	36.84 Å
Rg 误差 (实空间) rg_real_error	1.01 Å
I(0) (实空间) i0_real	2.7860e+08
I(0) 误差 (实空间) i0_real_error	4.3280e+06
Rg (倒空间) rg_reciprocal	36.82 Å
I(0) (倒空间) i0_reciprocal	278600000.0000
解质量估计 total_estimate	0.8833
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	42.6 Å
偏度 Skewness skewness	0.368
峰度 Kurtosis kurtosis	-0.362
角度范围 angular_range	— – 0.2150 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	42050000.0000
实空间数据点数 n_real_points	44
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.864; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.902

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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	Regulator of nonsense transcripts 1
分子量 formula_weight	70056.4 kDa
EC 编号 ec_number	3.6.1.-
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	9795

PLGSRYEDAYQYQNIFGPLVKLEADYDKKLKESQTQDNITVRWDLGLNKKRIAYFTLPKTDSDMRLMQGDEICLRYKGDLAPLWKGIGHVIKVPDNYGDEIAIELRSSVGAPVEVTHNFQVDFVWKSTSFDRMQSALKTFAVDETSVSGYIYHKLLGHEVEDVIIKCQLPKRFTAQGLPDLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPSNIAVDQLTEKIHQTGLKVVRLCAKSREAIDSPVSFLALHNQIRNMDSMPELQKLQQLKDETGELSSADEKRYRALKRTAERELLMNADVICCTCVGAGDPRLAKMQFRSILIDESTQATEPECMVPVVLGAKQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVLGIRPIRLQVQYRMHPALSAFPSNIFYEGSLQNGVTAADRVKKGFDFQWPQPDKPMFFYVTQGQEEIASSGTSYLNRTEAANVEKITTKLLKAGAKPDQIGIITPYEGQRSYLVQYMQFSGSLHTKLYQEVEIASVDAFQGREKDFIILSCVRANEHQGIGFLNDPRRLNVALTRARYGVIIVGNPKALSKQPLWNHLLNYYKEQKVLVEGPLNNLRESLMQFS

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

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	PHOSPHATE ION
分子量 formula_weight	95.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 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	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	233

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6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d2gk6a1
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.37.1.19 — Tandem AAA-ATPase domain

结构域编号 domain_id	d2gk6a2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.49 — Domain of alpha and beta subunits of F1 ATP synthase-like
超家族 Superfamily superfamily	b.49.4 — Upf1 barrel domain-like
家族 Family family	b.49.4.1 — Upf1 barrel domain-like

结构域编号 domain_id	d2gk6a3
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.37.1.19 — Tandem AAA-ATPase domain

结构域编号 domain_id	d2gk6a4
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d2gk6b1
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.37.1.19 — Tandem AAA-ATPase domain

结构域编号 domain_id	d2gk6b2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.49 — Domain of alpha and beta subunits of F1 ATP synthase-like
超家族 Superfamily superfamily	b.49.4 — Upf1 barrel domain-like
家族 Family family	b.49.4.1 — Upf1 barrel domain-like

结构域编号 domain_id	d2gk6b3
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.37.1.19 — Tandem AAA-ATPase domain

结构域编号 domain_id	d2gk6b4
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

CATH v4.4 (8 domains)

结构域编号 domain_id	2gk6A01
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	2gk6A02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
同源超家族 H-superfamily homologous superfamily	230 —

结构域编号 domain_id	2gk6A03
类 Class class	6 — Special
架构 Architecture architecture	10 — Helix non-globular
拓扑 Topology topology	140 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily	1240 —

结构域编号 domain_id	2gk6A04
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	2gk6B01
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	2gk6B02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
同源超家族 H-superfamily homologous superfamily	230 —

结构域编号 domain_id	2gk6B03
类 Class class	6 — Special
架构 Architecture architecture	10 — Helix non-globular
拓扑 Topology topology	140 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily	1240 —

结构域编号 domain_id	2gk6B04
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

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7. 引用文献 (1)

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晶胞边长 a length_a	63.284 Å
晶胞边长 b length_b	67.836 Å
晶胞边长 c length_c	87.250 Å
晶胞夹角 α angle_alpha	114.41 °
晶胞夹角 β angle_beta	90.13 °
晶胞夹角 γ angle_gamma	110.22 °
晶胞分子数 Z z_pdb	2

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

分辨率 resolution	2.400 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.2371
R_work r_work	0.2352
R_free r_free	0.2719

fit	/app/data/saxs_computation/gk/2gk6/2gk6.fit
pddf	/app/data/pr_computation/gk/2gk6/2gk6.pr.out
profile	/app/data/saxs_computation/gk/2gk6/2gk6.dat