1nvp

HUMAN TFIIA/TBP/DNA COMPLEX

Method: X-RAY DIFFRACTION D_max: 98.9 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

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1nvp
沉积日期 deposition_date	2003-02-04
结构标题 title	HUMAN TFIIA/TBP/DNA COMPLEX
关键词 keywords	TRANSCRIPTION REGULATION, DNA, COMPLEX, TRANSCRIPTION-DNA COMPLEX; TRANSCRIPTION/DNA
实验方法 method	X-RAY DIFFRACTION

▼

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	27.46 Å
回转半径 Rg (电子) rg_electron	27.99 Å
零角强度 I(0) i0	53323100.00
分子量 molecular_weight	52100.0 kDa
排除体积 excluded_volume	63074 Å³
包络体积 envelope_volume	80454 Å³
水化壳体积 shell_volume	25937 Å³
包络直径 envelope_diameter	102.3 Å
壳层 Rg shell_rg	32.56 Å
包络 Rg envelope_rg	28.02 Å
形状 Rg shape_rg	28.00 Å
总 Rg total_rg	28.39 Å
总原子数 total_atoms	3627
残基数 n_residues	401
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

▼

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	98.9 Å
Rg (实空间) rg_real	27.70 Å
Rg 误差 (实空间) rg_real_error	0.92 Å
I(0) (实空间) i0_real	5.3320e+07
I(0) 误差 (实空间) i0_real_error	7.6500e+05
Rg (倒空间) rg_reciprocal	27.63 Å
I(0) (倒空间) i0_reciprocal	53320000.0000
解质量估计 total_estimate	0.8344
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	27.3 Å
偏度 Skewness skewness	0.586
峰度 Kurtosis kurtosis	0.053
角度范围 angular_range	— – 0.2900 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	10250000.0000
实空间数据点数 n_real_points	59
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.712; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.810; Smooth: 0.895

▶

4. 晶体学与实验 4. Crystallography & Experiment

▶

5. 实体与聚合体信息 (7)

Entity 1 polymer

描述 description	5'-D(GPGPGPGPGPGPGPCPTPAPTPAPAPAPAPGP*G)-3'
分子量 formula_weight	5381.5 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
原子数 atom_count	3858

GGGGGGGCTATAAAAGG

Entity 2 polymer

描述 description	5'-D(CPCPTPTPTPTPAPTPAPGPCPCPCPCPCPCP*C)-3'
分子量 formula_weight	5034.3 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	F

CCTTTTATAGCCCCCCC

Entity 3 polymer

描述 description	TATA box binding protein
分子量 formula_weight	20443.3 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

SGIVPQLQNIVSTVNLGCKLDLKTIALRARNAEYNPKRFAAVIMRIREPRTTALIFSSGKMVCTGAKSEEQSRLAARKYARVVQKLGFPAKFLDFKIQNMVGSCDVKFPIRLEGLVLTHQQFSSYEPELFPGLIYRMIKPRIVLLIFVSGKVVLTGAKVRAEIYEAFENIYPILKGFRKTT

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	Escherichia coli

Entity 4 polymer

描述 description	Transcription initiation factor IIA alpha chain
分子量 formula_weight	6486.3 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	B

ANSANTNTVPKLYRSVIEDVINDVRDIFLDDGVDEQVLMELKTLWENKLMQSRAVDG

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	Escherichia coli

Entity 5 polymer

描述 description	Transcription initiation factor IIA beta chain
分子量 formula_weight	8687.4 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	C

GSGAEDGQVEEEPLNSEDDVSDEEGQELFDTENVVVCQYDKIHRSKNKWKFHLKDGIMNLNGRDYIFSKAIGDAEW

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	Escherichia coli

Entity 6 polymer

描述 description	Transcription initiation factor IIA gamma chain
分子量 formula_weight	12337.9 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

AYQLYRNTTLGNSLQESLDELIQSQQITPQLALQVLLQFDKAINAALAQRVRNRVNFRGSLNTYRFCDNVWTFVLNDVEFREVTELIKVDKVKIVACDGKNTGSNTTE

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	Escherichia coli

Entity 7 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	231

▼

6. 折叠分类 (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

结构域编号 domain_id	d1nvpa1
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	d1nvpa2
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	d1nvpb_
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	d1nvpc_
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

结构域编号 domain_id	d1nvpd1
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	d1nvpd2
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	1nvpA01
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	1nvpA02
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	1nvpB00
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	1nvpC00
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	1nvpD01
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	1nvpD02
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

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	59.624 Å
晶胞边长 b length_b	90.884 Å
晶胞边长 c length_c	125.256 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	2.100 Å
最低分辨率 resolution_low	39.000 Å
R 因子 r_factor	0.2290
R_work r_work	0.2290
R_free r_free	0.2470

fit	/app/data/saxs_computation/nv/1nvp/1nvp.fit
pddf	/app/data/pr_computation/nv/1nvp/1nvp.pr.out
profile	/app/data/saxs_computation/nv/1nvp/1nvp.dat

HUMAN TFIIA/TBP/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

5. 实体与聚合体信息 (7)

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 polymer

聚合体 Polymer

来源 Source

Entity 7 water

6. 折叠分类 (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)