2d1p

crystal structure of heterohexameric TusBCD proteins, which are crucial for the tRNA modification

Method: X-RAY DIFFRACTION D_max: 111.2 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

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2d1p
沉积日期 deposition_date	2005-08-30
结构标题 title	crystal structure of heterohexameric TusBCD proteins, which are crucial for the tRNA modification
关键词 keywords	tRNA modification, sulfur transfer, Structural genomics, TRANSLATION; TRANSLATION
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	33.96 Å
回转半径 Rg (电子) rg_electron	33.34 Å
零角强度 I(0) i0	190964000.00
分子量 molecular_weight	112340.0 kDa
排除体积 excluded_volume	141190 Å³
包络体积 envelope_volume	171560 Å³
水化壳体积 shell_volume	43609 Å³
包络直径 envelope_diameter	118.0 Å
壳层 Rg shell_rg	39.57 Å
包络 Rg envelope_rg	33.32 Å
形状 Rg shape_rg	33.34 Å
总 Rg total_rg	33.82 Å
总原子数 total_atoms	7930
残基数 n_residues	1029
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	111.2 Å
Rg (实空间) rg_real	34.07 Å
Rg 误差 (实空间) rg_real_error	0.79 Å
I(0) (实空间) i0_real	1.9100e+08
I(0) 误差 (实空间) i0_real_error	2.8900e+06
Rg (倒空间) rg_reciprocal	34.00 Å
I(0) (倒空间) i0_reciprocal	191000000.0000
解质量估计 total_estimate	0.8656
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	35.5 Å
偏度 Skewness skewness	0.443
峰度 Kurtosis kurtosis	-0.402
角度范围 angular_range	— – 0.2350 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	59240000.0000
实空间数据点数 n_real_points	48
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.840; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.945; Smooth: 0.782

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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 (5)

Entity 1 polymer

描述 description	Hypothetical UPF0163 protein yheN
分子量 formula_weight	15055.7 kDa
来源方法 src_method	man
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,D,G
原子数 atom_count	8214

MRGSHHHHHHGSMRFAIVVTGPAYGTQQASSAFQFAQALIADGHELSSVFFYREGVYNANQLTSPASDEFDLVRAWQQLNAQHGVALNICVAAALRRGVVDETEAGRLGLASSNLQQGFTLSGLGALAEASLTCDRVVQF

来源 Source

来源生物 organism	Escherichia coli
NCBI 分类编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 2 polymer

描述 description	Hypothetical UPF0116 protein yheM
分子量 formula_weight	13057.0 kDa
来源方法 src_method	man
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B,E,H

MKRIAFVFSTAPHGTAAGREGLDALLATSALTDDLAVFFIADGVFQLLPGQKPDAVLARDYIATFKLLGLYDIEQCWVCAASLRERGLDPQTPFVVEATPLEADALRRELANYDVILRF

来源 Source

来源生物 organism	Escherichia coli
NCBI 分类编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 3 polymer

描述 description	Hypothetical protein yheL
分子量 formula_weight	10729.3 kDa
来源方法 src_method	man
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	C,F,I

MLHTLHRSPWLTDFAALLRLLSEGDELLLLQDGVTAAVDGNRYLESLRNAPIKVYALNEDLIARGLTGQISNDIILIDYTDFVRLTVKHPSQMAW

来源 Source

来源生物 organism	Escherichia coli
NCBI 分类编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 4 non-polymer

描述 description	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 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	284

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6. 折叠分类 (SCOP + CATH) 21 domains

SCOP 2.08 (12 domains)

结构域编号 domain_id	d2d1pa1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.114 — DsrEFH-like
超家族 Superfamily superfamily	c.114.1 — DsrEFH-like
家族 Family family	c.114.1.1 — DsrEF-like

结构域编号 domain_id	d2d1pa2
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	d2d1pb1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.114 — DsrEFH-like
超家族 Superfamily superfamily	c.114.1 — DsrEFH-like
家族 Family family	c.114.1.1 — DsrEF-like

结构域编号 domain_id	d2d1pc1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.114 — DsrEFH-like
超家族 Superfamily superfamily	c.114.1 — DsrEFH-like
家族 Family family	c.114.1.2 — DsrH-like

结构域编号 domain_id	d2d1pd2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.114 — DsrEFH-like
超家族 Superfamily superfamily	c.114.1 — DsrEFH-like
家族 Family family	c.114.1.1 — DsrEF-like

结构域编号 domain_id	d2d1pd3
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	d2d1pe_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.114 — DsrEFH-like
超家族 Superfamily superfamily	c.114.1 — DsrEFH-like
家族 Family family	c.114.1.1 — DsrEF-like

结构域编号 domain_id	d2d1pf_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.114 — DsrEFH-like
超家族 Superfamily superfamily	c.114.1 — DsrEFH-like
家族 Family family	c.114.1.2 — DsrH-like

结构域编号 domain_id	d2d1pg2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.114 — DsrEFH-like
超家族 Superfamily superfamily	c.114.1 — DsrEFH-like
家族 Family family	c.114.1.1 — DsrEF-like

结构域编号 domain_id	d2d1pg3
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	d2d1ph_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.114 — DsrEFH-like
超家族 Superfamily superfamily	c.114.1 — DsrEFH-like
家族 Family family	c.114.1.1 — DsrEF-like

结构域编号 domain_id	d2d1pi_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.114 — DsrEFH-like
超家族 Superfamily superfamily	c.114.1 — DsrEFH-like
家族 Family family	c.114.1.2 — DsrH-like

CATH v4.4 (9 domains)

结构域编号 domain_id	2d1pA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1260 — Hypothetical Protein Ychn; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 — DsrEFH-like

结构域编号 domain_id	2d1pB00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1260 — Hypothetical Protein Ychn; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 — DsrEFH-like

结构域编号 domain_id	2d1pC00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1260 — Hypothetical Protein Ychn; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 — DsrEFH-like

结构域编号 domain_id	2d1pD00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1260 — Hypothetical Protein Ychn; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 — DsrEFH-like

结构域编号 domain_id	2d1pE00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1260 — Hypothetical Protein Ychn; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 — DsrEFH-like

结构域编号 domain_id	2d1pF00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1260 — Hypothetical Protein Ychn; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 — DsrEFH-like

结构域编号 domain_id	2d1pG00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1260 — Hypothetical Protein Ychn; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 — DsrEFH-like

结构域编号 domain_id	2d1pH00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1260 — Hypothetical Protein Ychn; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 — DsrEFH-like

结构域编号 domain_id	2d1pI00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1260 — Hypothetical Protein Ychn; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 — DsrEFH-like

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7. 引用文献 (1)

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晶胞边长 a length_a	141.392 Å
晶胞边长 b length_b	141.392 Å
晶胞边长 c length_c	135.686 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	24

空间群 space_group	P 41 21 2
空间群编号 int_tables_number	92
晶系 crystal_system	—

分辨率 resolution	2.150 Å
最低分辨率 resolution_low	50.000 Å
R 因子 r_factor	0.2094
R_work r_work	0.2094
R_free r_free	0.2423

fit	/app/data/saxs_computation/d1/2d1p/2d1p.fit
pddf	/app/data/pr_computation/d1/2d1p/2d1p.pr.out
profile	/app/data/saxs_computation/d1/2d1p/2d1p.dat

crystal structure of heterohexameric TusBCD proteins, which are crucial for the tRNA modification

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 (5)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 polymer

聚合体 Polymer

来源 Source

Entity 4 non-polymer

Entity 5 water

6. 折叠分类 (SCOP + CATH) 21 domains

SCOP 2.08 (12 domains)

CATH v4.4 (9 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)