SAXSdb — 1rm1

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1rm1
沉积日期 deposition_date	2003-11-26
结构标题 title	Structure of a Yeast TFIIA/TBP/TATA-box DNA Complex
关键词 keywords	Yeast TFIIA, TBP protein, ATA-box DNA, 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	27.87 Å
回转半径 Rg (电子) rg_electron	27.97 Å
零角强度 I(0) i0	62220200.00
分子量 molecular_weight	56054.0 kDa
排除体积 excluded_volume	67686 Å³
包络体积 envelope_volume	85744 Å³
水化壳体积 shell_volume	27318 Å³
包络直径 envelope_diameter	100.3 Å
壳层 Rg shell_rg	32.98 Å
包络 Rg envelope_rg	27.89 Å
形状 Rg shape_rg	28.01 Å
总 Rg total_rg	28.33 Å
总原子数 total_atoms	3899
残基数 n_residues	433
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	96.9 Å
Rg (实空间) rg_real	28.04 Å
Rg 误差 (实空间) rg_real_error	0.93 Å
I(0) (实空间) i0_real	6.2220e+07
I(0) 误差 (实空间) i0_real_error	8.8650e+05
Rg (倒空间) rg_reciprocal	27.99 Å
I(0) (倒空间) i0_reciprocal	62220000.0000
解质量估计 total_estimate	0.8547
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	30.6 Å
偏度 Skewness skewness	0.503
峰度 Kurtosis kurtosis	-0.112
角度范围 angular_range	— – 0.2850 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	10420000.0000
实空间数据点数 n_real_points	58
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.795; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.876; Smooth: 0.849

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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 (6)

Entity 1 polymer

描述 description	5'-D(APTPCPGPAPTPCPGPAPTPAPTPAPAPAPAPCPG)-3'
分子量 formula_weight	5532.6 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
原子数 atom_count	4200

ATCGATCGATATAAAACG

Entity 2 polymer

描述 description	5'-D(PCPGPTPTPTPTPAPTPAPTPCPGPAPTPCPGPAPT)-3'
分子量 formula_weight	5496.6 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	E

CGTTTTATATCGATCGAT

Entity 3 polymer

描述 description	TATA-box binding protein
分子量 formula_weight	27042.3 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

MADEERLKEFKEANKIVFDPNTRQVWENQNRDGTKPATTFQSEEDIKRAAPESEKDTSATSGIVPTLQNIVATVTLGCRLDLKTVALHARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVVTGAKSEDDSKLASRKYARIIQKIGFAAKFTDFKIQNIVGSCDVKFPIRLEGLAFSHGTFSSYEPELFPGLIYRMVKPKIVLLIFVSGKIVLTGAKQREEIYQAFEAIYPVLSEFRKM

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 4 polymer

描述 description	Transcription initiation factor IIA small chain
分子量 formula_weight	13473.1 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

MAVPGYYELYRRSTIGNSLVDALDTLISDGRIEASLAMRVLETFDKVVAETLKDNTQSKLTVKGNLDTYGFCDDVWTFIVKNCQVTVEDSHRDASQNGSGDSQSVISVDKLRIVACNSKKSE

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 5 polymer

描述 description	Transcription initiation factor IIA large chain
分子量 formula_weight	32230.8 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	C

MSNAEASRVYEIIVESVVNEVREDFENAGIDEQTLQDLKNIWQKKLTETKVTTFSWDNQFNEGNINGVQNDLNFNLATPGVNSSEFNIKEENTGNEGLILPNINSNNNIPHSGETNINTNTVEATNNSGATLNTNTSGNTNADVTSQPKIEVKPEIELTINNANITTVENIDDESEKKDDEEKEEDVEKTRKEKEQIEQVKLQAKKEKRSALLDTDEVGSELDDSDDDYLISEGEEDGPDENLMLCLYDKVTRTKARWKCSLKDGVVTINRNDYTFQKAQVEAEWV

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 6 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	301

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6. 折叠分类 (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1rm1a1
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	d1rm1a2
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	d1rm1b1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.32 — Transcription factor IIA (TFIIA), alpha-helical domain
超家族 Superfamily superfamily	a.32.1 — Transcription factor IIA (TFIIA), alpha-helical domain
家族 Family family	a.32.1.1 — Transcription factor IIA (TFIIA), alpha-helical domain

结构域编号 domain_id	d1rm1b2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.56 — Transcription factor IIA (TFIIA), beta-barrel domain
超家族 Superfamily superfamily	b.56.1 — Transcription factor IIA (TFIIA), beta-barrel domain
家族 Family family	b.56.1.1 — Transcription factor IIA (TFIIA), beta-barrel domain

CATH v4.4 (6 domains)

结构域编号 domain_id	1rm1A01
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	1rm1A02
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	1rm1B01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily	190 — Transcription factor IIA gamma subunit, alpha-helical domain

结构域编号 domain_id	1rm1B02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	18 — TATA box binding Protein, subunit D; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Transcription factor IIA (TFIIA), beta-barrel domain

结构域编号 domain_id	1rm1C01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily	100 —

结构域编号 domain_id	1rm1C02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	18 — TATA box binding Protein, subunit D; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Transcription factor IIA (TFIIA), beta-barrel domain

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7. 引用文献 (1)

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晶胞边长 a length_a	173.250 Å
晶胞边长 b length_b	173.250 Å
晶胞边长 c length_c	164.070 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	18

空间群 space_group	H 3 2
空间群编号 int_tables_number	155
晶系 crystal_system	—

分辨率 resolution	2.500 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.1890
R_work r_work	0.1860
R_free r_free	0.2520

fit	/app/data/saxs_computation/rm/1rm1/1rm1.fit
pddf	/app/data/pr_computation/rm/1rm1/1rm1.pr.out
profile	/app/data/saxs_computation/rm/1rm1/1rm1.dat

Structure of a Yeast TFIIA/TBP/TATA-box DNA 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

衍射实验 Diffraction

5. 实体与聚合体信息 (6)

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

Entity 6 water

6. 折叠分类 (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

CATH v4.4 (6 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)