SAXSdb — 2gjk

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2gjk
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	hupf1, 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	26.23 Å
回转半径 Rg (电子) rg_electron	25.31 Å
零角强度 I(0) i0	78558600.00
分子量 molecular_weight	69397.0 kDa
排除体积 excluded_volume	87083 Å³
包络体积 envelope_volume	107280 Å³
水化壳体积 shell_volume	34276 Å³
包络直径 envelope_diameter	83.9 Å
壳层 Rg shell_rg	33.57 Å
包络 Rg envelope_rg	25.38 Å
形状 Rg shape_rg	25.34 Å
总 Rg total_rg	26.12 Å
总原子数 total_atoms	4876
残基数 n_residues	614
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	78.1 Å
Rg (实空间) rg_real	26.07 Å
Rg 误差 (实空间) rg_real_error	0.41 Å
I(0) (实空间) i0_real	7.8560e+07
I(0) 误差 (实空间) i0_real_error	1.0730e+06
Rg (倒空间) rg_reciprocal	26.12 Å
I(0) (倒空间) i0_reciprocal	78560000.0000
解质量估计 total_estimate	0.8361
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	32.5 Å
偏度 Skewness skewness	0.138
峰度 Kurtosis kurtosis	-0.536
角度范围 angular_range	— – 0.3000 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	16200000.0000
实空间数据点数 n_real_points	61
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.960; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.000

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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 (4)

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	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	4986

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	1

Entity 3 non-polymer

描述 description	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
分子量 formula_weight	506.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 4 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	110

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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	d2gjka1
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	d2gjka2
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	d2gjka3
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	d2gjka4
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 (4 domains)

结构域编号 domain_id	2gjkA01
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	2gjkA02
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	2gjkA03
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	2gjkA04
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	188.979 Å
晶胞边长 b length_b	188.979 Å
晶胞边长 c length_c	44.872 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	8

空间群 space_group	P 43 21 2
空间群编号 int_tables_number	96
晶系 crystal_system	—

分辨率 resolution	2.600 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.2462
R_work r_work	0.2449
R_free r_free	0.2710

fit	/app/data/saxs_computation/gj/2gjk/2gjk.fit
pddf	/app/data/pr_computation/gj/2gjk/2gjk.pr.out
profile	/app/data/saxs_computation/gj/2gjk/2gjk.dat

Structural and functional insights into the human Upf1 helicase core

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