1ngm

Crystal structure of a yeast Brf1-TBP-DNA ternary complex

Method: X-RAY DIFFRACTION D_max: 252.8 Å Quality: REASONABLE

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	1ngm
沉积日期 deposition_date	2002-12-17
结构标题 title	Crystal structure of a yeast Brf1-TBP-DNA ternary complex
关键词 keywords	TRANSCRIPTION, TFIIIB, TBP, BRF, BRF1, TAF, 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	77.99 Å
回转半径 Rg (电子) rg_electron	81.82 Å
零角强度 I(0) i0	476402000.00
分子量 molecular_weight	155990.0 kDa
排除体积 excluded_volume	184890 Å³
包络体积 envelope_volume	370480 Å³
水化壳体积 shell_volume	49811 Å³
包络直径 envelope_diameter	273.0 Å
壳层 Rg shell_rg	46.93 Å
包络 Rg envelope_rg	82.77 Å
形状 Rg shape_rg	81.87 Å
总 Rg total_rg	80.72 Å
总原子数 total_atoms	10800
残基数 n_residues	1122
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	252.8 Å
Rg (实空间) rg_real	79.52 Å
Rg 误差 (实空间) rg_real_error	2.94 Å
I(0) (实空间) i0_real	4.7620e+08
I(0) 误差 (实空间) i0_real_error	1.1370e+07
Rg (倒空间) rg_reciprocal	72.24 Å
I(0) (倒空间) i0_reciprocal	469300000.0000
解质量估计 total_estimate	0.6304
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	3
主峰位置 r_peak_primary	37.9 Å
偏度 Skewness skewness	0.651
峰度 Kurtosis kurtosis	-0.359
角度范围 angular_range	— – 0.1000 Å⁻¹
当前正则化参数 α current_alpha	0.0005
最高正则化参数 α highest_alpha	8085000.0000
实空间数据点数 n_real_points	21
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.099; Stabil: 0.980; Sysdev: 1.000; Positv: 1.000; Valcen: 0.185; Smooth: 0.767

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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	5'-D(CPTPAPTPAPAPAPAPAPAPAPTPGPTPTPTPTPTP*T)-3'
分子量 formula_weight	5816.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polydeoxyribonucleotide
链编号 strand_id	C,G,K,O
原子数 atom_count	10800

CTATAAAAAAATGTTTTTT

Entity 2 polymer

描述 description	5'-D(APAPAPAPAPAPCPAPTPTPTPTPTPTPTPAPTPAP*G)-3'
分子量 formula_weight	5825.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polydeoxyribonucleotide
链编号 strand_id	D,H,L,P

AAAAAACATTTTTTTATAG

Entity 3 polymer

描述 description	Transcription initiation factor TFIID
分子量 formula_weight	20120.8 kDa
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,E,I,M

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 4 polymer

描述 description	Transcription factor IIIB BRF1 subunit
分子量 formula_weight	8337.2 kDa
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B,F,J,N

GSYCPRNLHLLPTTDTYLSKVSDDPDNLEDVDDEELNAHLLNEEASKLKERIWIGLNADFLLEQESKRLKQE

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

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6. 折叠分类 (SCOP + CATH) 26 domains

SCOP 2.08 (14 domains)

结构域编号 domain_id	d1ngma1
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	d1ngma2
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	d1ngmb1
类 Class class	j — Peptides
折叠类型 Fold fold	j.104 — TBP-binding domain of the transcription factor IIIb Brf1 subunit
超家族 Superfamily superfamily	j.104.1 — TBP-binding domain of the transcription factor IIIb Brf1 subunit
家族 Family family	j.104.1.1 — TBP-binding domain of the transcription factor IIIb Brf1 subunit

结构域编号 domain_id	d1ngmb2
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d1ngme1
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	d1ngme2
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	d1ngmf1
类 Class class	j — Peptides
折叠类型 Fold fold	j.104 — TBP-binding domain of the transcription factor IIIb Brf1 subunit
超家族 Superfamily superfamily	j.104.1 — TBP-binding domain of the transcription factor IIIb Brf1 subunit
家族 Family family	j.104.1.1 — TBP-binding domain of the transcription factor IIIb Brf1 subunit

结构域编号 domain_id	d1ngmf2
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d1ngmi1
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	d1ngmi2
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	d1ngmj_
类 Class class	j — Peptides
折叠类型 Fold fold	j.104 — TBP-binding domain of the transcription factor IIIb Brf1 subunit
超家族 Superfamily superfamily	j.104.1 — TBP-binding domain of the transcription factor IIIb Brf1 subunit
家族 Family family	j.104.1.1 — TBP-binding domain of the transcription factor IIIb Brf1 subunit

结构域编号 domain_id	d1ngmm1
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	d1ngmm2
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	d1ngmn_
类 Class class	j — Peptides
折叠类型 Fold fold	j.104 — TBP-binding domain of the transcription factor IIIb Brf1 subunit
超家族 Superfamily superfamily	j.104.1 — TBP-binding domain of the transcription factor IIIb Brf1 subunit
家族 Family family	j.104.1.1 — TBP-binding domain of the transcription factor IIIb Brf1 subunit

CATH v4.4 (12 domains)

结构域编号 domain_id	1ngmA01
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	1ngmA02
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	1ngmB00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	650 — Single helix bin

结构域编号 domain_id	1ngmE01
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	1ngmE02
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	1ngmF00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	650 — Single helix bin

结构域编号 domain_id	1ngmI01
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	1ngmI02
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	1ngmJ00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	650 — Single helix bin

结构域编号 domain_id	1ngmM01
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	1ngmM02
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	1ngmN00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	650 — Single helix bin

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7. 引用文献 (1)

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晶胞边长 a length_a	93.610 Å
晶胞边长 b length_b	152.600 Å
晶胞边长 c length_c	256.638 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	16

空间群 space_group	P 21 21 2
空间群编号 int_tables_number	18
晶系 crystal_system	—

分辨率 resolution	2.950 Å
最低分辨率 resolution_low	50.000 Å
R 因子 r_factor	0.2780
R_work r_work	0.2760
R_free r_free	0.3080

fit	/app/data/saxs_computation/ng/1ngm/1ngm.fit
pddf	/app/data/pr_computation/ng/1ngm/1ngm.pr.out
profile	/app/data/saxs_computation/ng/1ngm/1ngm.dat

Crystal structure of a yeast Brf1-TBP-DNA ternary 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 (4)

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

6. 折叠分类 (SCOP + CATH) 26 domains

SCOP 2.08 (14 domains)

CATH v4.4 (12 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)