1nex

Crystal Structure of ScSkp1-ScCdc4-CPD peptide complex

Method: X-RAY DIFFRACTION D_max: 139.7 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	1nex
沉积日期 deposition_date	2002-12-12
结构标题 title	Crystal Structure of ScSkp1-ScCdc4-CPD peptide complex
关键词 keywords	WD 40 domain, phospho-peptide complex, E3 ubiquitin ligase, LIGASE, CELL CYCLE; LIGASE, CELL CYCLE
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	44.35 Å
回转半径 Rg (电子) rg_electron	43.95 Å
零角强度 I(0) i0	259410000.00
分子量 molecular_weight	133590.0 kDa
排除体积 excluded_volume	167640 Å³
包络体积 envelope_volume	238070 Å³
水化壳体积 shell_volume	46794 Å³
包络直径 envelope_diameter	138.0 Å
壳层 Rg shell_rg	47.19 Å
包络 Rg envelope_rg	42.29 Å
形状 Rg shape_rg	43.91 Å
总 Rg total_rg	44.24 Å
总原子数 total_atoms	9363
残基数 n_residues	1139
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	139.7 Å
Rg (实空间) rg_real	44.45 Å
Rg 误差 (实空间) rg_real_error	1.28 Å
I(0) (实空间) i0_real	2.5940e+08
I(0) 误差 (实空间) i0_real_error	4.5390e+06
Rg (倒空间) rg_reciprocal	44.35 Å
I(0) (倒空间) i0_reciprocal	259400000.0000
解质量估计 total_estimate	0.8302
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	38.8 Å
偏度 Skewness skewness	0.233
峰度 Kurtosis kurtosis	-0.761
角度范围 angular_range	— – 0.1800 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	16830000.0000
实空间数据点数 n_real_points	37
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.960; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.909; 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	Centromere DNA-binding protein complex CBF3 subunit D
分子量 formula_weight	19739.0 kDa
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,C
原子数 atom_count	9435

GAHMVTSNVVLVSGEGERFTVDKKIAERSLLLKNYLNDMGDDDDEDDDEIVMPVPNVRSSVLQKVIEWAEHHRDSNFPDEDDDDSRKSAPVDSWDREFLKVDQEMLYEIILAANYLNIKPLLDAGCKVVAEMIRGRSPEEIRRTFNIVNDFTPEEEAAIRRENEWAEDR

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;baker's yeast ;
NCBI 分类编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli

Entity 2 polymer

描述 description	CDC4 protein
分子量 formula_weight	53143.5 kDa
突变 mutation	C608L
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	B,D

GAGTLIKDNLKRDLITSLPFEISLKIFNYLQFEDIINSLGVSQNWNKIIRKSTSLWKKLLISENFVSPKGFNSLNLKLSQKYPKLSQQDRLRLSFLENIFILKNWYNPKFVPQRTTLRGHMTSVITCLQFEDNYVITGADDKMIRVYDSINKKFLLQLSGHDGGVWALKYAHGGILVSGSTDRTVRVWDIKKGCCTHVFEGHNSTVRCLDIVEYKNIKYIVTGSRDNTLHVWKLPKESSVPDHGEEHDYPLVFHTPEENPYFVGVLRGHMASVRTVSGHGNIVVSGSYDNTLIVWDVAQMKCLYILSGHTDRIYSTIYDHERKRCISASMDTTIRIWDLENGELMYTLQGHTALVGLLRLSDKFLVSAAADGSIRGWDANDYSRKFSYHHTNLSAITTFYVSDNILVSGSENQFNIYNLRSGKLVHANILKDADQIWSVNFKGKTLVAAVEKDGQSFLEILDFS

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;baker's yeast ;
NCBI 分类编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli

Entity 3 polymer

描述 description	GLL(TPO)PPQSG
分子量 formula_weight	949.0 kDa
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	E,F

GLLTPPQSG

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	72

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6. 折叠分类 (SCOP + CATH) 14 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d1nexa1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.157 — Skp1 dimerisation domain-like
超家族 Superfamily superfamily	a.157.1 — Skp1 dimerisation domain-like
家族 Family family	a.157.1.1 — Skp1 dimerisation domain-like

结构域编号 domain_id	d1nexa2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.42 — POZ domain
超家族 Superfamily superfamily	d.42.1 — POZ domain
家族 Family family	d.42.1.1 — BTB/POZ domain

结构域编号 domain_id	d1nexb1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.158 — F-box domain
超家族 Superfamily superfamily	a.158.1 — F-box domain
家族 Family family	a.158.1.1 — F-box domain

结构域编号 domain_id	d1nexb2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.69 — 7-bladed beta-propeller
超家族 Superfamily superfamily	b.69.4 — WD40 repeat-like
家族 Family family	b.69.4.1 — WD40-repeat

结构域编号 domain_id	d1nexc1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.157 — Skp1 dimerisation domain-like
超家族 Superfamily superfamily	a.157.1 — Skp1 dimerisation domain-like
家族 Family family	a.157.1.1 — Skp1 dimerisation domain-like

结构域编号 domain_id	d1nexc2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.42 — POZ domain
超家族 Superfamily superfamily	d.42.1 — POZ domain
家族 Family family	d.42.1.1 — BTB/POZ domain

结构域编号 domain_id	d1nexd1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.158 — F-box domain
超家族 Superfamily superfamily	a.158.1 — F-box domain
家族 Family family	a.158.1.1 — F-box domain

结构域编号 domain_id	d1nexd2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.69 — 7-bladed beta-propeller
超家族 Superfamily superfamily	b.69.4 — WD40 repeat-like
家族 Family family	b.69.4.1 — WD40-repeat

CATH v4.4 (6 domains)

结构域编号 domain_id	1nexA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	710 — Potassium Channel Kv1.1; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Potassium Channel Kv1.1; Chain A

结构域编号 domain_id	1nexB01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1280 — Monooxygenase
同源超家族 H-superfamily homologous superfamily	50 —

结构域编号 domain_id	1nexB02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	130 — 7 Propeller
拓扑 Topology topology	10 — Methylamine Dehydrogenase; Chain H
同源超家族 H-superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

结构域编号 domain_id	1nexC00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	710 — Potassium Channel Kv1.1; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Potassium Channel Kv1.1; Chain A

结构域编号 domain_id	1nexD01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1280 — Monooxygenase
同源超家族 H-superfamily homologous superfamily	50 —

结构域编号 domain_id	1nexD02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	130 — 7 Propeller
拓扑 Topology topology	10 — Methylamine Dehydrogenase; Chain H
同源超家族 H-superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

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7. 引用文献 (1)

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晶胞边长 a length_a	107.669 Å
晶胞边长 b length_b	107.669 Å
晶胞边长 c length_c	168.300 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	120.00 °
晶胞分子数 Z z_pdb	6

空间群 space_group	P 32
空间群编号 int_tables_number	145
晶系 crystal_system	—

分辨率 resolution	2.700 Å
最低分辨率 resolution_low	19.990 Å
R 因子 r_factor	0.2390
R_work r_work	0.2390
R_free r_free	0.2730

fit	/app/data/saxs_computation/ne/1nex/1nex.fit
pddf	/app/data/pr_computation/ne/1nex/1nex.pr.out
profile	/app/data/saxs_computation/ne/1nex/1nex.dat

Crystal Structure of ScSkp1-ScCdc4-CPD peptide complex

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

5. 实体与聚合体信息 (4)

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

Entity 4 water

6. 折叠分类 (SCOP + CATH) 14 domains

SCOP 2.08 (8 domains)

CATH v4.4 (6 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)