2gjw

RNA Recognition and Cleavage by an Splicing Endonuclease

Method: X-RAY DIFFRACTION D_max: 159.0 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	2gjw
沉积日期 deposition_date	2006-03-31
结构标题 title	RNA Recognition and Cleavage by an Splicing Endonuclease
关键词 keywords	Bulge-Helix-Bulge RNA-protein complex, Splicing Endonuclease Af, Hydrolase-RNA COMPLEX; Hydrolase/RNA
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	47.28 Å
回转半径 Rg (电子) rg_electron	46.88 Å
零角强度 I(0) i0	484997000.00
分子量 molecular_weight	168260.0 kDa
排除体积 excluded_volume	204600 Å³
包络体积 envelope_volume	283470 Å³
水化壳体积 shell_volume	50920 Å³
包络直径 envelope_diameter	170.3 Å
壳层 Rg shell_rg	50.47 Å
包络 Rg envelope_rg	46.17 Å
形状 Rg shape_rg	46.82 Å
总 Rg total_rg	47.19 Å
总原子数 total_atoms	11778
残基数 n_residues	1296
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	159.0 Å
Rg (实空间) rg_real	47.71 Å
Rg 误差 (实空间) rg_real_error	1.92 Å
I(0) (实空间) i0_real	4.8500e+08
I(0) 误差 (实空间) i0_real_error	9.8450e+06
Rg (倒空间) rg_reciprocal	47.29 Å
I(0) (倒空间) i0_reciprocal	484700000.0000
解质量估计 total_estimate	0.7855
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	33.7 Å
偏度 Skewness skewness	0.370
峰度 Kurtosis kurtosis	-0.800
角度范围 angular_range	— – 0.1650 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	69890000.0000
实空间数据点数 n_real_points	34
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.591; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.735; Smooth: 0.698

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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'-R(GPCPGPAPCPCPGPAPCPCPAP(DU)PAPGPCPUPGPCP*A)-3'
分子量 formula_weight	6059.7 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	E,I
原子数 atom_count	11778

GCGACCGACCAUAGCUGCA

Entity 2 polymer

描述 description	5'-R(UPGPCPAPGPCPGPGPUPCPAP(A23))-3'
分子量 formula_weight	3913.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	F,J

UGCAGCGGUCAA

Entity 3 polymer

描述 description	5'-R(APGPGPUPCPGP*C)-3'
分子量 formula_weight	2236.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	H,L

AGGUCGC

Entity 4 polymer

描述 description	tRNA-splicing endonuclease
分子量 formula_weight	37105.4 kDa
EC 编号 ec_number	3.1.27.9
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,B,C,D

MHHHHHHHHIGGDFAVVKAKKSLERRGFGVKRGDKIYLHPLEVVYLQIKGIESFGELEDVLSWAESRMEDFSTYYFVYEDLRDRGNKVKIQGEFLLTKKPYLPISERKTIRMEEIAEKARNFDELRLAVVDEESEITYFRVYEPDMMGEQKEELPEIAGVLSDEYVITKQTEIFSRYFYGSEKGDLVTLSLIESLYLLDLGKLNLLNADREELVKRAREVERNFDRRYEVYRNLKERGFVVKTGFKFGSEFRVYRKVESVDDLPHSEYLVDIADSREIRLIDLARAVRLAQNVRKRMVFAYGKNYLCFERVKV

来源 Source

来源生物 organism	Archaeoglobus fulgidus
NCBI 分类编号 ncbi_taxonomy_id	2234
宿主生物 host_organism	Escherichia coli

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6. 折叠分类 (SCOP + CATH) 31 domains

SCOP 2.08 (19 domains)

结构域编号 domain_id	d2gjwa1
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	d2gjwa2
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	d2gjwa3
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	d2gjwa4
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	d2gjwa5
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	d2gjwb1
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	d2gjwb2
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	d2gjwb3
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	d2gjwb4
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	d2gjwb5
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	d2gjwc1
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	d2gjwc2
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	d2gjwc3
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	d2gjwc4
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	d2gjwc5
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	d2gjwd1
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	d2gjwd2
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	d2gjwd3
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	d2gjwd4
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 (12 domains)

结构域编号 domain_id	2gjwA01
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	2gjwA02
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	2gjwA03
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	2gjwB01
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	2gjwB02
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	2gjwB03
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	2gjwC01
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	2gjwC02
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	2gjwC03
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	2gjwD01
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	2gjwD02
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	2gjwD03
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	90.073 Å
晶胞边长 b length_b	140.357 Å
晶胞边长 c length_c	82.048 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	111.69 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

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	2.850 Å
最低分辨率 resolution_low	35.090 Å
R 因子 r_factor	0.2499
R_work r_work	0.2474
R_free r_free	0.2965

fit	/app/data/saxs_computation/gj/2gjw/2gjw.fit
pddf	/app/data/pr_computation/gj/2gjw/2gjw.pr.out
profile	/app/data/saxs_computation/gj/2gjw/2gjw.dat

RNA Recognition and Cleavage by an Splicing Endonuclease

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

Entity 4 polymer

聚合体 Polymer

来源 Source

6. 折叠分类 (SCOP + CATH) 31 domains

SCOP 2.08 (19 domains)

CATH v4.4 (12 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)