1tf6

CO-CRYSTAL STRUCTURE OF XENOPUS TFIIIA ZINC FINGER DOMAIN BOUND TO THE 5S RIBOSOMAL RNA GENE INTERNAL CONTROL REGION

Method: X-RAY DIFFRACTION D_max: 111.8 Å Quality: EXCELLENT

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	1tf6
沉积日期 deposition_date	1998-03-02
结构标题 title	CO-CRYSTAL STRUCTURE OF XENOPUS TFIIIA ZINC FINGER DOMAIN BOUND TO THE 5S RIBOSOMAL RNA GENE INTERNAL CONTROL REGION
关键词 keywords	;COMPLEX (TRANSCRIPTION REGULATION-DNA), RNA POLYMERASE III, TRANSCRIPTION INITIATION, ZINC FINGER PROTEIN, 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	34.98 Å
回转半径 Rg (电子) rg_electron	35.30 Å
零角强度 I(0) i0	186071000.00
分子量 molecular_weight	81078.0 kDa
排除体积 excluded_volume	89194 Å³
包络体积 envelope_volume	148050 Å³
水化壳体积 shell_volume	37227 Å³
包络直径 envelope_diameter	110.8 Å
壳层 Rg shell_rg	39.29 Å
包络 Rg envelope_rg	34.16 Å
形状 Rg shape_rg	35.32 Å
总 Rg total_rg	35.50 Å
总原子数 total_atoms	5495
残基数 n_residues	485
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	111.8 Å
Rg (实空间) rg_real	34.86 Å
Rg 误差 (实空间) rg_real_error	1.08 Å
I(0) (实空间) i0_real	1.8610e+08
I(0) 误差 (实空间) i0_real_error	3.2280e+06
Rg (倒空间) rg_reciprocal	34.93 Å
I(0) (倒空间) i0_reciprocal	186100000.0000
解质量估计 total_estimate	0.9058
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	47.2 Å
偏度 Skewness skewness	0.108
峰度 Kurtosis kurtosis	-0.546
角度范围 angular_range	— – 0.2250 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	5488000.0000
实空间数据点数 n_real_points	46
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.941; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.949

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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	;DNA (5'-D(APCPGPGPGPCPCPTPGPGPTPTPAPGPTPAPC PCPTPGPGPAP* TPGPGPGPAPGPAPCPC)-3') ;
分子量 formula_weight	9634.2 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	B,E
原子数 atom_count	5495

ACGGGCCTGGTTAGTACCTGGATGGGAGACC

Entity 2 polymer

描述 description	;DNA (5'-D(TPGPGPTPCPTPCPCPCPAPTPCPCPAPGPGPT PAPCPTPAPAP* CPCPAPGPGPCPCPCPG)-3') ;
分子量 formula_weight	9434.1 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,F

TGGTCTCCCATCCAGGTACTAACCAGGCCCG

Entity 3 polymer

描述 description	PROTEIN (TRANSCRIPTION FACTOR IIIA)
分子量 formula_weight	22126.5 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,D

MGEKALPVVYKRYICSFADCGAAYNKNWKLQAHLCKHTGEKPFPCKEEGCEKGFTSLHHLTRHSLTHTGEKNFTCDSDGCDLRFTTKANMKKHFNRFHNIKICVYVCHFENCGKAFKKHNQLKVHQFSHTQQLPYECPHEGCDKRFSLPSRLKRHEKVHAGYPCKKDDSCSFVGKTWTLYLKHVAECHQD

来源 Source

来源生物 organism	Xenopus laevis
通用名 common_name	African clawed frog
NCBI 分类编号 ncbi_taxonomy_id	8355
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 4 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	12

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6. 折叠分类 (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

结构域编号 domain_id	d1tf6a1
类 Class class	g — Small proteins
折叠类型 Fold fold	g.37 — beta-beta-alpha zinc fingers
超家族 Superfamily superfamily	g.37.1 — beta-beta-alpha zinc fingers
家族 Family family	g.37.1.1 — Classic zinc finger, C2H2

结构域编号 domain_id	d1tf6a2
类 Class class	g — Small proteins
折叠类型 Fold fold	g.37 — beta-beta-alpha zinc fingers
超家族 Superfamily superfamily	g.37.1 — beta-beta-alpha zinc fingers
家族 Family family	g.37.1.1 — Classic zinc finger, C2H2

结构域编号 domain_id	d1tf6a3
类 Class class	g — Small proteins
折叠类型 Fold fold	g.37 — beta-beta-alpha zinc fingers
超家族 Superfamily superfamily	g.37.1 — beta-beta-alpha zinc fingers
家族 Family family	g.37.1.1 — Classic zinc finger, C2H2

结构域编号 domain_id	d1tf6a4
类 Class class	g — Small proteins
折叠类型 Fold fold	g.37 — beta-beta-alpha zinc fingers
超家族 Superfamily superfamily	g.37.1 — beta-beta-alpha zinc fingers
家族 Family family	g.37.1.1 — Classic zinc finger, C2H2

结构域编号 domain_id	d1tf6a5
类 Class class	g — Small proteins
折叠类型 Fold fold	g.37 — beta-beta-alpha zinc fingers
超家族 Superfamily superfamily	g.37.1 — beta-beta-alpha zinc fingers
家族 Family family	g.37.1.1 — Classic zinc finger, C2H2

结构域编号 domain_id	d1tf6a6
类 Class class	g — Small proteins
折叠类型 Fold fold	g.37 — beta-beta-alpha zinc fingers
超家族 Superfamily superfamily	g.37.1 — beta-beta-alpha zinc fingers
家族 Family family	g.37.1.1 — Classic zinc finger, C2H2

结构域编号 domain_id	d1tf6d1
类 Class class	g — Small proteins
折叠类型 Fold fold	g.37 — beta-beta-alpha zinc fingers
超家族 Superfamily superfamily	g.37.1 — beta-beta-alpha zinc fingers
家族 Family family	g.37.1.1 — Classic zinc finger, C2H2

结构域编号 domain_id	d1tf6d2
类 Class class	g — Small proteins
折叠类型 Fold fold	g.37 — beta-beta-alpha zinc fingers
超家族 Superfamily superfamily	g.37.1 — beta-beta-alpha zinc fingers
家族 Family family	g.37.1.1 — Classic zinc finger, C2H2

结构域编号 domain_id	d1tf6d3
类 Class class	g — Small proteins
折叠类型 Fold fold	g.37 — beta-beta-alpha zinc fingers
超家族 Superfamily superfamily	g.37.1 — beta-beta-alpha zinc fingers
家族 Family family	g.37.1.1 — Classic zinc finger, C2H2

结构域编号 domain_id	d1tf6d4
类 Class class	g — Small proteins
折叠类型 Fold fold	g.37 — beta-beta-alpha zinc fingers
超家族 Superfamily superfamily	g.37.1 — beta-beta-alpha zinc fingers
家族 Family family	g.37.1.1 — Classic zinc finger, C2H2

结构域编号 domain_id	d1tf6d5
类 Class class	g — Small proteins
折叠类型 Fold fold	g.37 — beta-beta-alpha zinc fingers
超家族 Superfamily superfamily	g.37.1 — beta-beta-alpha zinc fingers
家族 Family family	g.37.1.1 — Classic zinc finger, C2H2

结构域编号 domain_id	d1tf6d6
类 Class class	g — Small proteins
折叠类型 Fold fold	g.37 — beta-beta-alpha zinc fingers
超家族 Superfamily superfamily	g.37.1 — beta-beta-alpha zinc fingers
家族 Family family	g.37.1.1 — Classic zinc finger, C2H2

CATH v4.4 (12 domains)

结构域编号 domain_id	1tf6A01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	160 — Double Stranded RNA Binding Domain
同源超家族 H-superfamily homologous superfamily	60 — Classic Zinc Finger

结构域编号 domain_id	1tf6A02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	160 — Double Stranded RNA Binding Domain
同源超家族 H-superfamily homologous superfamily	60 — Classic Zinc Finger

结构域编号 domain_id	1tf6A03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	160 — Double Stranded RNA Binding Domain
同源超家族 H-superfamily homologous superfamily	60 — Classic Zinc Finger

结构域编号 domain_id	1tf6A04
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	160 — Double Stranded RNA Binding Domain
同源超家族 H-superfamily homologous superfamily	60 — Classic Zinc Finger

结构域编号 domain_id	1tf6A05
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	160 — Double Stranded RNA Binding Domain
同源超家族 H-superfamily homologous superfamily	60 — Classic Zinc Finger

结构域编号 domain_id	1tf6A06
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	160 — Double Stranded RNA Binding Domain
同源超家族 H-superfamily homologous superfamily	60 — Classic Zinc Finger

结构域编号 domain_id	1tf6D01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	160 — Double Stranded RNA Binding Domain
同源超家族 H-superfamily homologous superfamily	60 — Classic Zinc Finger

结构域编号 domain_id	1tf6D02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	160 — Double Stranded RNA Binding Domain
同源超家族 H-superfamily homologous superfamily	60 — Classic Zinc Finger

结构域编号 domain_id	1tf6D03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	160 — Double Stranded RNA Binding Domain
同源超家族 H-superfamily homologous superfamily	60 — Classic Zinc Finger

结构域编号 domain_id	1tf6D04
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	160 — Double Stranded RNA Binding Domain
同源超家族 H-superfamily homologous superfamily	60 — Classic Zinc Finger

结构域编号 domain_id	1tf6D05
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	160 — Double Stranded RNA Binding Domain
同源超家族 H-superfamily homologous superfamily	60 — Classic Zinc Finger

结构域编号 domain_id	1tf6D06
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	160 — Double Stranded RNA Binding Domain
同源超家族 H-superfamily homologous superfamily	60 — Classic Zinc Finger

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7. 引用文献 (1)

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晶胞边长 a length_a	64.180 Å
晶胞边长 b length_b	64.712 Å
晶胞边长 c length_c	78.035 Å
晶胞夹角 α angle_alpha	90.07 °
晶胞夹角 β angle_beta	92.98 °
晶胞夹角 γ angle_gamma	102.95 °
晶胞分子数 Z z_pdb	2

空间群 space_group	P 1
空间群编号 int_tables_number	1
晶系 crystal_system	—

分辨率 resolution	3.100 Å
最低分辨率 resolution_low	8.000 Å
R 因子 r_factor	0.3080
R_work r_work	0.3080
R_free r_free	0.3630

fit	/app/data/saxs_computation/tf/1tf6/1tf6.fit
pddf	/app/data/pr_computation/tf/1tf6/1tf6.pr.out
profile	/app/data/saxs_computation/tf/1tf6/1tf6.dat

CO-CRYSTAL STRUCTURE OF XENOPUS TFIIIA ZINC FINGER DOMAIN BOUND TO THE 5S RIBOSOMAL RNA GENE INTERNAL CONTROL REGION

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 non-polymer

6. 折叠分类 (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)