SAXSdb — 1ytb

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1ytb
沉积日期 deposition_date	1994-09-28
结构标题 title	CRYSTAL STRUCTURE OF A YEAST TBP/TATA-BOX COMPLEX
关键词 keywords	PROTEIN-DNA COMPLEX, TRANSCRIPTION-DNA COMPLEX; TRANSCRIPTION/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	26.93 Å
回转半径 Rg (电子) rg_electron	26.76 Å
零角强度 I(0) i0	73025600.00
分子量 molecular_weight	58204.0 kDa
排除体积 excluded_volume	69128 Å³
包络体积 envelope_volume	93103 Å³
水化壳体积 shell_volume	29480 Å³
包络直径 envelope_diameter	98.1 Å
壳层 Rg shell_rg	33.64 Å
包络 Rg envelope_rg	26.22 Å
形状 Rg shape_rg	26.77 Å
总 Rg total_rg	27.37 Å
总原子数 total_atoms	4026
残基数 n_residues	418
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	96.8 Å
Rg (实空间) rg_real	26.85 Å
Rg 误差 (实空间) rg_real_error	0.97 Å
I(0) (实空间) i0_real	7.3030e+07
I(0) 误差 (实空间) i0_real_error	1.2020e+06
Rg (倒空间) rg_reciprocal	26.88 Å
I(0) (倒空间) i0_reciprocal	73030000.0000
解质量估计 total_estimate	0.7694
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	36.1 Å
偏度 Skewness skewness	0.245
峰度 Kurtosis kurtosis	-0.251
角度范围 angular_range	— – 0.2950 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	12490000.0000
实空间数据点数 n_real_points	60
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.685; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.944; 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 (3)

Entity 1 polymer

描述 description	DNA (29MER)
分子量 formula_weight	8987.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polydeoxyribonucleotide
链编号 strand_id	C,D
原子数 atom_count	4539

GTATATAAAACGGGTGGCGTTTTATATAC

Entity 2 polymer

描述 description	PROTEIN (TATA BINDING PROTEIN (TBP))
分子量 formula_weight	20120.8 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,B

SGIVPTLQNIVATVTLGCRLDLKTVALHARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVVTGAKSEDDSKLASRKYARIIQKIGFAAKFTDFKIQNIVGSCDVKFPIRLEGLAFSHGTFSSYEPELFPGLIYRMVKPKIVLLIFVSGKIVLTGAKQREEIYQAFEAIYPVLSEFRKM

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 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	513

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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	d1ytba1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.129 — TBP-like
超家族 Superfamily superfamily	d.129.1 — TATA-box binding protein-like
家族 Family family	d.129.1.1 — TATA-box binding protein (TBP), C-terminal domain

结构域编号 domain_id	d1ytba2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.129 — TBP-like
超家族 Superfamily superfamily	d.129.1 — TATA-box binding protein-like
家族 Family family	d.129.1.1 — TATA-box binding protein (TBP), C-terminal domain

结构域编号 domain_id	d1ytbb1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.129 — TBP-like
超家族 Superfamily superfamily	d.129.1 — TATA-box binding protein-like
家族 Family family	d.129.1.1 — TATA-box binding protein (TBP), C-terminal domain

结构域编号 domain_id	d1ytbb2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.129 — TBP-like
超家族 Superfamily superfamily	d.129.1 — TATA-box binding protein-like
家族 Family family	d.129.1.1 — TATA-box binding protein (TBP), C-terminal domain

CATH v4.4 (4 domains)

结构域编号 domain_id	1ytbA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	310 — TATA-Binding Protein
同源超家族 H-superfamily homologous superfamily	10 — TATA-Binding Protein

结构域编号 domain_id	1ytbA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	310 — TATA-Binding Protein
同源超家族 H-superfamily homologous superfamily	10 — TATA-Binding Protein

结构域编号 domain_id	1ytbB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	310 — TATA-Binding Protein
同源超家族 H-superfamily homologous superfamily	10 — TATA-Binding Protein

结构域编号 domain_id	1ytbB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	310 — TATA-Binding Protein
同源超家族 H-superfamily homologous superfamily	10 — TATA-Binding Protein

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7. 引用文献 (1)

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晶胞边长 a length_a	100.770 Å
晶胞边长 b length_b	100.770 Å
晶胞边长 c length_c	66.500 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
空间群编号 int_tables_number	78
晶系 crystal_system	—

分辨率 resolution	1.800 Å
最低分辨率 resolution_low	6.000 Å
R 因子 r_factor	0.2010
R_work r_work	0.2010
R_free r_free	0.2610

fit	/app/data/saxs_computation/yt/1ytb/1ytb.fit
pddf	/app/data/pr_computation/yt/1ytb/1ytb.pr.out
profile	/app/data/saxs_computation/yt/1ytb/1ytb.dat

CRYSTAL STRUCTURE OF A YEAST TBP/TATA-BOX 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 (3)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 water

6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)