SAXSdb — 1jey

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1jey
沉积日期 deposition_date	2001-06-19
结构标题 title	Crystal Structure of the Ku heterodimer bound to DNA
关键词 keywords	;double-strand DNA break repair, non-homologous end-joining, protein-nucleic acid complex, alpha/beta domain, beta barrel, helical C-terminal arm, SAP domain, DNA BINDING PROTEIN-DNA COMPLEX ;; DNA BINDING PROTEIN/DNA
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	34.32 Å
回转半径 Rg (电子) rg_electron	33.77 Å
零角强度 I(0) i0	294718000.00
分子量 molecular_weight	131880.0 kDa
排除体积 excluded_volume	162560 Å³
包络体积 envelope_volume	214750 Å³
水化壳体积 shell_volume	52630 Å³
包络直径 envelope_diameter	123.6 Å
壳层 Rg shell_rg	40.87 Å
包络 Rg envelope_rg	33.37 Å
形状 Rg shape_rg	33.78 Å
总 Rg total_rg	34.26 Å
总原子数 total_atoms	9217
残基数 n_residues	1072
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	115.0 Å
Rg (实空间) rg_real	34.28 Å
Rg 误差 (实空间) rg_real_error	0.96 Å
I(0) (实空间) i0_real	2.9470e+08
I(0) 误差 (实空间) i0_real_error	5.4290e+06
Rg (倒空间) rg_reciprocal	34.31 Å
I(0) (倒空间) i0_reciprocal	294700000.0000
解质量估计 total_estimate	0.8681
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	42.5 Å
偏度 Skewness skewness	0.376
峰度 Kurtosis kurtosis	-0.084
角度范围 angular_range	— – 0.2300 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	75550000.0000
实空间数据点数 n_real_points	47
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.797; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.896

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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	;DNA (5'-D(GPTPTPTPTPTPAPGPTPTPTPAPTPTPGPGPGPCPGPCP*G)-3') ;
分子量 formula_weight	6506.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polydeoxyribonucleotide
链编号 strand_id	C
原子数 atom_count	9472

GTTTTTAGTTTATTGGGCGCG

Entity 2 polymer

描述 description	DNA (34-MER)
分子量 formula_weight	10325.7 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polydeoxyribonucleotide
链编号 strand_id	D

CGCGCCCAGCTTTCCCAGCTAATAAACTAAAAAC

Entity 3 polymer

描述 description	Ku70
分子量 formula_weight	69945.0 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	A

MSGWESYYKTEGDEEAEEEQEENLEASGDYKYSGRDSLIFLVDASKAMFESQSEDELTPFDMSIQCIQSVYISKIISSDRDLLAVVFYGTEKDKNSVNFKNIYVLQELDNPGAKRILELDQFKGQQGQKRFQDMMGHGSDYSLSEVLWVCANLFSDVQFKMSHKRIMLFTNEDNPHGNDSAKASRARTKAGDLRDTGIFLDLMHLKKPGGFDISLFYRDIISIAEDEDLRVHFEESSKLEDLLRKVRAKETRKRALSRLKLKLNKDIVISVGIYNLVQKALKPPPIKLYRETNEPVKTKTRTFNTSTGGLLLPSDTKRSQIYGSRQIILEKEETEELKRFDDPGLMLMGFKPLVLLKKHHYLRPSLFVYPEESLVIGSSTLFSALLIKCLEKEVAALCRYTPRRNIPPYFVALVPQEEELDDQKIQVTPPGFQLVFLPFADDKRKMPFTEKIMATPEQVGKMKAIVEKLRFTYRSDSFENPVLQQHFRNLEALALDLMEPEQAVDLTLPKVEAMNKRLGSLVDEFKELVYPPDYNPEGKVTKRKHDNEGSGSKRPKVEYSEEELKTHISKGTLGKFTVPMLKEACRAYGLKSGLKKQELLEALTKHFQD

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	Spodoptera frugiperda

Entity 4 polymer

描述 description	Ku80
分子量 formula_weight	64190.5 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	B

MVRSGNKAAVVLCMDVGFTMSNSIPGIESPFEQAKKVITMFVQRQVFAENKDEIALVLFGTDGTDNPLSGGDQYQNITVHRHLMLPDFDLLEDIESKIQPGSQQADFLDALIVSMDVIQHETIGKKFEKRHIEIFTDLSSRFSKSQLDIIIHSLKKCDISLQFFLPFSLGKEDGSGDRGDGPFRLGGHGPSFPLKGITEQQKEGLEIVKMVMISLEGEDGLDEIYSFSESLRKLCVFKKIERHSIHWPCRLTIGSNLSIRIAAYKSILQERVKKTWTVVDAKTLKKEDIQKETVYCLNDDDETEVLKEDIIQGFRYGSDIVPFSKVDEEQMKYKSEGKCFSVLGFCKSSQVQRRFFMGNQVLKVFAARDDEAAAVALSSLIHALDDLDMVAIVRYAYDKRANPQVGVAFPHIKHNYECLVYVQLPFMEDLRQYMFSSLKNSKKYAPTEAQLNAVDALIDSMSLAKKDEKTDTLEDLFPTTKIPNPRFQRLFQCLLHRALHPREPLPPIQQHIWNMLNPPAEVTTKSQIPLSKIKTLFPLIEAKKKDQVTAQEIFQDNHEDGPTAK

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	Spodoptera frugiperda

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	255

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6. 折叠分类 (SCOP + CATH) 11 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1jeya1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.131 — SPOC domain-like
超家族 Superfamily superfamily	b.131.1 — SPOC domain-like
家族 Family family	b.131.1.1 — Ku70 subunit middle domain

结构域编号 domain_id	d1jeya2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.62 — vWA-like
超家族 Superfamily superfamily	c.62.1 — vWA-like
家族 Family family	c.62.1.3 — Ku70 subunit N-terminal domain

结构域编号 domain_id	d1jeyb1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.131 — SPOC domain-like
超家族 Superfamily superfamily	b.131.1 — SPOC domain-like
家族 Family family	b.131.1.2 — Ku80 subunit middle domain

结构域编号 domain_id	d1jeyb2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.62 — vWA-like
超家族 Superfamily superfamily	c.62.1 — vWA-like
家族 Family family	c.62.1.4 — Ku80 subunit N-terminal domain

CATH v4.4 (7 domains)

结构域编号 domain_id	1jeyA01
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	410 — von Willebrand factor, type A domain

结构域编号 domain_id	1jeyA02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	290 — Ku70; Chain: A; Domain 2
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1jeyA03
类 Class class	4 — Few Secondary Structures
架构 Architecture architecture	10 — Irregular
拓扑 Topology topology	970 — Ku70, bridge and pillars
同源超家族 H-superfamily homologous superfamily	10 — Ku70, bridge and pillars

结构域编号 domain_id	1jeyA04
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1600 — Ku70; Chain: A; domain 4
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1jeyB01
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	410 — von Willebrand factor, type A domain

结构域编号 domain_id	1jeyB02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	290 — Ku70; Chain: A; Domain 2
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1jeyB03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1600 — Ku70; Chain: A; domain 4
同源超家族 H-superfamily homologous superfamily	10 —

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7. 引用文献 (1)

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晶胞边长 a length_a	83.920 Å
晶胞边长 b length_b	126.305 Å
晶胞边长 c length_c	126.436 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 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	2.500 Å
最低分辨率 resolution_low	24.740 Å
R 因子 r_factor	0.2200
R_work r_work	0.2180
R_free r_free	0.2800

fit	/app/data/saxs_computation/je/1jey/1jey.fit
pddf	/app/data/pr_computation/je/1jey/1jey.pr.out
profile	/app/data/saxs_computation/je/1jey/1jey.dat

Crystal Structure of the Ku heterodimer bound to DNA

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 (5)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

Entity 3 polymer

聚合体 Polymer

来源 Source

Entity 4 polymer

聚合体 Polymer

来源 Source

Entity 5 water

6. 折叠分类 (SCOP + CATH) 11 domains

SCOP 2.08 (4 domains)

CATH v4.4 (7 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)