SAXSdb — 2fo1

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2fo1
沉积日期 deposition_date	2006-01-12
结构标题 title	Crystal Structure of the CSL-Notch-Mastermind ternary complex bound to DNA
关键词 keywords	beta-barrel, PROTEIN-DNA COMPLEX, DOUBLE HELIX, ankyrin repeat, GENE REGULATION-SIGNALLING PROTEIN-DNA COMPLEX; GENE REGULATION/SIGNALLING 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	31.18 Å
回转半径 Rg (电子) rg_electron	29.84 Å
零角强度 I(0) i0	189170000.00
分子量 molecular_weight	99936.0 kDa
排除体积 excluded_volume	120880 Å³
包络体积 envelope_volume	159130 Å³
水化壳体积 shell_volume	43377 Å³
包络直径 envelope_diameter	105.6 Å
壳层 Rg shell_rg	37.99 Å
包络 Rg envelope_rg	29.80 Å
形状 Rg shape_rg	29.80 Å
总 Rg total_rg	30.61 Å
总原子数 total_atoms	6939
残基数 n_residues	815
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	100.6 Å
Rg (实空间) rg_real	31.04 Å
Rg 误差 (实空间) rg_real_error	0.65 Å
I(0) (实空间) i0_real	1.8920e+08
I(0) 误差 (实空间) i0_real_error	2.6980e+06
Rg (倒空间) rg_reciprocal	31.10 Å
I(0) (倒空间) i0_reciprocal	189200000.0000
解质量估计 total_estimate	0.8961
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	39.5 Å
偏度 Skewness skewness	0.209
峰度 Kurtosis kurtosis	-0.395
角度范围 angular_range	— – 0.2550 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	25680000.0000
实空间数据点数 n_real_points	52
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.895; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.962

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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	5'-D(TPTPAPCPTPGPTPGPGPGPAPAPAPGP*A)-3'
分子量 formula_weight	4673.1 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	B
原子数 atom_count	6939

TTACTGTGGGAAAGA

Entity 2 polymer

描述 description	5'-D(APAPTPCPTPTPTPCPCPCPAPCPAPGP*T)-3'
分子量 formula_weight	4503.9 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

AATCTTTCCCACAGT

Entity 3 polymer

描述 description	Lin-12 and glp-1 phenotype protein 1, isoform b
分子量 formula_weight	53761.6 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

GPLGSGDSVQSLTSDRMIDFLSNKEKYECVISIFHAKVAQKSYGNEKRFFCPPPCIYLIGQGWKLKKDRVAQLYKTLKASAQKDAAIENDPIHEQQATELVAYIGIGSDTSERQQLDFSTGKVRHPGDQRQDPNIYDYCAAKTLYISDSDKRKYFDLNAQFFYGCGMEIGGFVSQRIKVISKPSKKKQSMKNTDCKYLCIASGTKVALFNRLRSQTVSTRYLHVEGNAFHASSTKWGAFTIHLFDDERGLQETDNFAVRDGFVYYGSVVKLVDSVTGIALPRLRIRKVDKQQVILDASCSEEPVSQLHKCAFQMIDNELVYLCLSHDKIIQHQATAINEHRHQINDGAAWTIISTDKAEYRFFEAMGQVANPISPCPVVGSLEVDGHGEASRVELHGRDFKPNLKVWFGATPVETTFRSEESLHCSIPPVSQVRNEQTHWMFTNRTTGDVEVPISLVRDDGVVYSSGLTFSYKSLER

来源 Source

来源生物 organism	Caenorhabditis elegans
NCBI 分类编号 ncbi_taxonomy_id	6239
宿主生物 host_organism	Escherichia coli

Entity 4 polymer

描述 description	Protein lag-3
分子量 formula_weight	9755.6 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	D

SPNPEDEPTIGDLNAFHSGEELHRQRSELARANYEKARPEMIANQRAVTAHLFNRYTEDEERKRVEQQKNKEAMNASTSAPTSSR

来源 Source

来源生物 organism	Caenorhabditis elegans
NCBI 分类编号 ncbi_taxonomy_id	6239
宿主生物 host_organism	Escherichia coli

Entity 5 polymer

描述 description	Lin-12 protein
分子量 formula_weight	42457.4 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	E

GSGNRTRKRRMINASVWMPPMENEEKNRKNHQSITSSQHSLLEASYDGYIKRQRNELQHYSLYPNPQGYGNGNDFLGDFNHTNLQIPTEPEPESPIKLHTEAAGSYAITEPITRESVNIIDPRHNRTVLHWIASNSSAEKSEDLIVHEAKECIAAGADVNAMDCDENTPLMLAVLARRRRLVAYLMKAGADPTIYNKSERSALHQAAANRDFGMMVYMLNSTKLKGDIEELDRNGMTALMIVAHNEGRDQVASAKLLVEKGAKVDYDGAARKDSEKYKGRTALHYAAQVSNMPIVKYLVGEKGSNKDKQDEDGKTPIMLAAQEGRIEVVMYLIQQGASVEAVDATDHTARQLAQANNHHNIVDIFDRCRPERE

来源 Source

来源生物 organism	Caenorhabditis elegans
NCBI 分类编号 ncbi_taxonomy_id	6239
宿主生物 host_organism	Escherichia coli

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6. 折叠分类 (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

结构域编号 domain_id	d2fo1a1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.18 — E set domains
家族 Family family	b.1.18.1 — NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain

结构域编号 domain_id	d2fo1a2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.2 — Common fold of diphtheria toxin/transcription factors/cytochrome f
超家族 Superfamily superfamily	b.2.5 — p53-like transcription factors
家族 Family family	b.2.5.8 — DNA-binding protein LAG-1 (CSL)

结构域编号 domain_id	d2fo1a3
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.42 — beta-Trefoil
超家族 Superfamily superfamily	b.42.7 — DNA-binding protein LAG-1 (CSL)
家族 Family family	b.42.7.1 — DNA-binding protein LAG-1 (CSL)

结构域编号 domain_id	d2fo1d1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.137 — Non-globular all-alpha subunits of globular proteins
超家族 Superfamily superfamily	a.137.14 — Lag-3 N-terminal region
家族 Family family	a.137.14.1 — Lag-3 N-terminal region

结构域编号 domain_id	d2fo1e1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.211 — beta-hairpin-alpha-hairpin repeat
超家族 Superfamily superfamily	d.211.1 — Ankyrin repeat
家族 Family family	d.211.1.1 — Ankyrin repeat

CATH v4.4 (5 domains)

结构域编号 domain_id	2fo1A01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	1450 — LAG1, DNA binding domain

结构域编号 domain_id	2fo1A02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	80 — Trefoil
拓扑 Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
同源超家族 H-superfamily homologous superfamily	50 —

结构域编号 domain_id	2fo1A03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

结构域编号 domain_id	2fo1D00
类 Class class	6 — Special
架构 Architecture architecture	10 — Helix non-globular
拓扑 Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	990 —

结构域编号 domain_id	2fo1E00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	25 — Alpha Horseshoe
拓扑 Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
同源超家族 H-superfamily homologous superfamily	20 — Ankyrin repeat-containing domain

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7. 引用文献 (1)

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晶胞边长 a length_a	66.093 Å
晶胞边长 b length_b	96.785 Å
晶胞边长 c length_c	243.538 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	3.120 Å
最低分辨率 resolution_low	43.510 Å
R 因子 r_factor	0.2730
R_work r_work	0.2730
R_free r_free	0.3400

fit	/app/data/saxs_computation/fo/2fo1/2fo1.fit
pddf	/app/data/pr_computation/fo/2fo1/2fo1.pr.out
profile	/app/data/saxs_computation/fo/2fo1/2fo1.dat

Crystal Structure of the CSL-Notch-Mastermind ternary complex 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 polymer

聚合体 Polymer

来源 Source

6. 折叠分类 (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

CATH v4.4 (5 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)