1gd8

THE CRYSTAL STRUCTURE OF BACTERIA-SPECIFIC L17 RIBOSOMAL PROTEIN.

Method: X-RAY DIFFRACTION D_max: 144.8 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	1gd8
沉积日期 deposition_date	2000-09-22
结构标题 title	THE CRYSTAL STRUCTURE OF BACTERIA-SPECIFIC L17 RIBOSOMAL PROTEIN.
关键词 keywords	;TWO DOMAINS, RIBOSOMAL PROTEIN S8-LIKE DOMAIN, TRP REPRESSOR-LIKE DOMAIN, HELIX-TURN-HELIX MOTIF, TWO TYPES OF DIMERS, FOUR DIMERS OF EACH TYPE., RIKEN Structural Genomics/Proteomics Initiative, RSGI, Structural Genomics, RIBOSOME ;; RIBOSOME
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	39.37 Å
回转半径 Rg (电子) rg_electron	39.53 Å
零角强度 I(0) i0	182347000.00
分子量 molecular_weight	109000.0 kDa
排除体积 excluded_volume	137320 Å³
包络体积 envelope_volume	192640 Å³
水化壳体积 shell_volume	44127 Å³
包络直径 envelope_diameter	154.5 Å
壳层 Rg shell_rg	41.31 Å
包络 Rg envelope_rg	39.45 Å
形状 Rg shape_rg	39.50 Å
总 Rg total_rg	39.74 Å
总原子数 total_atoms	7695
残基数 n_residues	945
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	144.8 Å
Rg (实空间) rg_real	39.71 Å
Rg 误差 (实空间) rg_real_error	1.83 Å
I(0) (实空间) i0_real	1.8230e+08
I(0) 误差 (实空间) i0_real_error	3.6010e+06
Rg (倒空间) rg_reciprocal	39.50 Å
I(0) (倒空间) i0_reciprocal	182300000.0000
解质量估计 total_estimate	0.8359
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	43.5 Å
偏度 Skewness skewness	0.543
峰度 Kurtosis kurtosis	-0.053
角度范围 angular_range	— – 0.2000 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	15270000.0000
实空间数据点数 n_real_points	41
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.694; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.845; Smooth: 0.937

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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 (2)

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6. 折叠分类 (SCOP + CATH) 18 domains

SCOP 2.08 (9 domains)

结构域编号 domain_id	d1gd8a_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.188 — Prokaryotic ribosomal protein L17
超家族 Superfamily superfamily	d.188.1 — Prokaryotic ribosomal protein L17
家族 Family family	d.188.1.1 — Prokaryotic ribosomal protein L17

结构域编号 domain_id	d1gd8b_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.188 — Prokaryotic ribosomal protein L17
超家族 Superfamily superfamily	d.188.1 — Prokaryotic ribosomal protein L17
家族 Family family	d.188.1.1 — Prokaryotic ribosomal protein L17

结构域编号 domain_id	d1gd8c_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.188 — Prokaryotic ribosomal protein L17
超家族 Superfamily superfamily	d.188.1 — Prokaryotic ribosomal protein L17
家族 Family family	d.188.1.1 — Prokaryotic ribosomal protein L17

结构域编号 domain_id	d1gd8d_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.188 — Prokaryotic ribosomal protein L17
超家族 Superfamily superfamily	d.188.1 — Prokaryotic ribosomal protein L17
家族 Family family	d.188.1.1 — Prokaryotic ribosomal protein L17

结构域编号 domain_id	d1gd8e_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.188 — Prokaryotic ribosomal protein L17
超家族 Superfamily superfamily	d.188.1 — Prokaryotic ribosomal protein L17
家族 Family family	d.188.1.1 — Prokaryotic ribosomal protein L17

结构域编号 domain_id	d1gd8f_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.188 — Prokaryotic ribosomal protein L17
超家族 Superfamily superfamily	d.188.1 — Prokaryotic ribosomal protein L17
家族 Family family	d.188.1.1 — Prokaryotic ribosomal protein L17

结构域编号 domain_id	d1gd8g_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.188 — Prokaryotic ribosomal protein L17
超家族 Superfamily superfamily	d.188.1 — Prokaryotic ribosomal protein L17
家族 Family family	d.188.1.1 — Prokaryotic ribosomal protein L17

结构域编号 domain_id	d1gd8h_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.188 — Prokaryotic ribosomal protein L17
超家族 Superfamily superfamily	d.188.1 — Prokaryotic ribosomal protein L17
家族 Family family	d.188.1.1 — Prokaryotic ribosomal protein L17

结构域编号 domain_id	d1gd8i_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.188 — Prokaryotic ribosomal protein L17
超家族 Superfamily superfamily	d.188.1 — Prokaryotic ribosomal protein L17
家族 Family family	d.188.1.1 — Prokaryotic ribosomal protein L17

CATH v4.4 (9 domains)

结构域编号 domain_id	1gd8A00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1030 — 50s Ribosomal Protein L17; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 — Ribosomal protein L17

结构域编号 domain_id	1gd8B00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1030 — 50s Ribosomal Protein L17; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 — Ribosomal protein L17

结构域编号 domain_id	1gd8C00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1030 — 50s Ribosomal Protein L17; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 — Ribosomal protein L17

结构域编号 domain_id	1gd8D00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1030 — 50s Ribosomal Protein L17; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 — Ribosomal protein L17

结构域编号 domain_id	1gd8E00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1030 — 50s Ribosomal Protein L17; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 — Ribosomal protein L17

结构域编号 domain_id	1gd8F00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1030 — 50s Ribosomal Protein L17; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 — Ribosomal protein L17

结构域编号 domain_id	1gd8G00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1030 — 50s Ribosomal Protein L17; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 — Ribosomal protein L17

结构域编号 domain_id	1gd8H00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1030 — 50s Ribosomal Protein L17; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 — Ribosomal protein L17

结构域编号 domain_id	1gd8I00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1030 — 50s Ribosomal Protein L17; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 — Ribosomal protein L17

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7. 引用文献 (1)

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晶胞边长 a length_a	109.239 Å
晶胞边长 b length_b	109.239 Å
晶胞边长 c length_c	128.841 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	36

空间群 space_group	P 41
空间群编号 int_tables_number	76
晶系 crystal_system	—

分辨率 resolution	2.300 Å
最低分辨率 resolution_low	50.000 Å
R 因子 r_factor	0.2130
R_work r_work	0.2100
R_free r_free	0.2540

描述 description	50S RIBOSOMAL PROTEIN L17
分子量 formula_weight	13750.1 kDa
来源方法 src_method	man
拷贝数 entity_count	9

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F,G,H,I
原子数 atom_count	7852

THE CRYSTAL STRUCTURE OF BACTERIA-SPECIFIC L17 RIBOSOMAL PROTEIN.

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 (2)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 water

6. 折叠分类 (SCOP + CATH) 18 domains

SCOP 2.08 (9 domains)

CATH v4.4 (9 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)

来源生物 organism	Thermus thermophilus
NCBI 分类编号 ncbi_taxonomy_id	274
宿主生物 host_organism	Escherichia coli

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	157

fit	/app/data/saxs_computation/gd/1gd8/1gd8.fit
pddf	/app/data/pr_computation/gd/1gd8/1gd8.pr.out
profile	/app/data/saxs_computation/gd/1gd8/1gd8.dat