1r11

Structure Determination of the Dimeric Endonuclease in a Pseudo-face-centerd P21 space group

Method: X-RAY DIFFRACTION D_max: 106.6 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	1r11
沉积日期 deposition_date	2003-09-23
结构标题 title	Structure Determination of the Dimeric Endonuclease in a Pseudo-face-centerd P21 space group
关键词 keywords	RNA splicing; endonuclease; x-ray crystallography, TRANSLATION, HYDROLASE; TRANSLATION, HYDROLASE
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	29.28 Å
回转半径 Rg (电子) rg_electron	28.92 Å
零角强度 I(0) i0	78144300.00
分子量 molecular_weight	71396.0 kDa
排除体积 excluded_volume	90177 Å³
包络体积 envelope_volume	110490 Å³
水化壳体积 shell_volume	32746 Å³
包络直径 envelope_diameter	115.8 Å
壳层 Rg shell_rg	35.11 Å
包络 Rg envelope_rg	29.36 Å
形状 Rg shape_rg	28.90 Å
总 Rg total_rg	29.57 Å
总原子数 total_atoms	5042
残基数 n_residues	606
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	106.6 Å
Rg (实空间) rg_real	29.41 Å
Rg 误差 (实空间) rg_real_error	1.09 Å
I(0) (实空间) i0_real	7.8140e+07
I(0) 误差 (实空间) i0_real_error	1.1090e+06
Rg (倒空间) rg_reciprocal	29.35 Å
I(0) (倒空间) i0_reciprocal	78140000.0000
解质量估计 total_estimate	0.7552
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	3
主峰位置 r_peak_primary	29.6 Å
偏度 Skewness skewness	0.532
峰度 Kurtosis kurtosis	-0.049
角度范围 angular_range	— – 0.2700 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	60490000.0000
实空间数据点数 n_real_points	55
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.644; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.885; Smooth: 0.000

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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 (1)

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6. 折叠分类 (SCOP + CATH) 14 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d1r11a1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.52 — Restriction endonuclease-like
超家族 Superfamily superfamily	c.52.2 — tRNA-intron endonuclease catalytic domain-like
家族 Family family	c.52.2.1 — tRNA-intron endonuclease catalytic domain-like

结构域编号 domain_id	d1r11a2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.52 — Restriction endonuclease-like
超家族 Superfamily superfamily	c.52.2 — tRNA-intron endonuclease catalytic domain-like
家族 Family family	c.52.2.1 — tRNA-intron endonuclease catalytic domain-like

结构域编号 domain_id	d1r11a3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.75 — MutS N-terminal domain-like
超家族 Superfamily superfamily	d.75.1 — tRNA-intron endonuclease N-terminal domain-like
家族 Family family	d.75.1.1 — tRNA-intron endonuclease N-terminal domain-like

结构域编号 domain_id	d1r11a4
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.75 — MutS N-terminal domain-like
超家族 Superfamily superfamily	d.75.1 — tRNA-intron endonuclease N-terminal domain-like
家族 Family family	d.75.1.1 — tRNA-intron endonuclease N-terminal domain-like

结构域编号 domain_id	d1r11b1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.52 — Restriction endonuclease-like
超家族 Superfamily superfamily	c.52.2 — tRNA-intron endonuclease catalytic domain-like
家族 Family family	c.52.2.1 — tRNA-intron endonuclease catalytic domain-like

结构域编号 domain_id	d1r11b2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.52 — Restriction endonuclease-like
超家族 Superfamily superfamily	c.52.2 — tRNA-intron endonuclease catalytic domain-like
家族 Family family	c.52.2.1 — tRNA-intron endonuclease catalytic domain-like

结构域编号 domain_id	d1r11b3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.75 — MutS N-terminal domain-like
超家族 Superfamily superfamily	d.75.1 — tRNA-intron endonuclease N-terminal domain-like
家族 Family family	d.75.1.1 — tRNA-intron endonuclease N-terminal domain-like

结构域编号 domain_id	d1r11b4
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.75 — MutS N-terminal domain-like
超家族 Superfamily superfamily	d.75.1 — tRNA-intron endonuclease N-terminal domain-like
家族 Family family	d.75.1.1 — tRNA-intron endonuclease N-terminal domain-like

CATH v4.4 (6 domains)

结构域编号 domain_id	1r11A01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1350 — Trna Endonuclease; Chain: A, domain 1
同源超家族 H-superfamily homologous superfamily	150 —

结构域编号 domain_id	1r11A02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1170 — MutS, DNA mismatch repair protein, domain I
同源超家族 H-superfamily homologous superfamily	20 — tRNA intron endonuclease, N-terminal domain

结构域编号 domain_id	1r11A03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1350 — Trna Endonuclease; Chain: A, domain 1
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1r11B01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1350 — Trna Endonuclease; Chain: A, domain 1
同源超家族 H-superfamily homologous superfamily	150 —

结构域编号 domain_id	1r11B02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1170 — MutS, DNA mismatch repair protein, domain I
同源超家族 H-superfamily homologous superfamily	20 — tRNA intron endonuclease, N-terminal domain

结构域编号 domain_id	1r11B03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1350 — Trna Endonuclease; Chain: A, domain 1
同源超家族 H-superfamily homologous superfamily	10 —

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7. 引用文献 (1)

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晶胞边长 a length_a	52.412 Å
晶胞边长 b length_b	74.169 Å
晶胞边长 c length_c	84.855 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	106.13 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	—

分辨率 resolution	2.700 Å
最低分辨率 resolution_low	26.660 Å
R 因子 r_factor	0.2369
R_work r_work	0.2306
R_free r_free	0.2927

描述 description	tRNA-intron endonuclease
分子量 formula_weight	36000.2 kDa
EC 编号 ec_number	3.1.27.9
来源方法 src_method	man
拷贝数 entity_count	2

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	5042

Structure Determination of the Dimeric Endonuclease in a Pseudo-face-centerd P21 space group

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 (1)

Entity 1 polymer

聚合体 Polymer

来源 Source

6. 折叠分类 (SCOP + CATH) 14 domains

SCOP 2.08 (8 domains)

CATH v4.4 (6 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)

来源生物 organism	Archaeoglobus fulgidus
NCBI 分类编号 ncbi_taxonomy_id	224325
宿主生物 host_organism	Escherichia coli

fit	/app/data/saxs_computation/r1/1r11/1r11.fit
pddf	/app/data/pr_computation/r1/1r11/1r11.pr.out
profile	/app/data/saxs_computation/r1/1r11/1r11.dat