2jl9

Structural explanation for the role of Mn in the activity of phi6 RNA- dependent RNA polymerase

Method: X-RAY DIFFRACTION D_max: 181.9 Å Quality: REASONABLE

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	2jl9
沉积日期 deposition_date	2008-09-05
结构标题 title	Structural explanation for the role of Mn in the activity of phi6 RNA- dependent RNA polymerase
关键词 keywords	;NUCLEOTIDE-BINDING, NUCLEOTIDYLTRANSFERASE, RNA-DEPENDENT RNA POLYMERASE, TRANSFERASE, METAL-BINDING, OLIGONUCLEOTIDE, RNA-DIRECTED RNA POLYMERASE, RNA REPLICATION, POLYMERASE-COMPLEX, VIRION, MANGANESE, MAGNESIUM, POLYMERASE ;; TRANSFERASE
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	54.28 Å
回转半径 Rg (电子) rg_electron	55.16 Å
零角强度 I(0) i0	718811000.00
分子量 molecular_weight	222050.0 kDa
排除体积 excluded_volume	277470 Å³
包络体积 envelope_volume	383740 Å³
水化壳体积 shell_volume	64921 Å³
包络直径 envelope_diameter	193.8 Å
壳层 Rg shell_rg	48.97 Å
包络 Rg envelope_rg	54.41 Å
形状 Rg shape_rg	55.16 Å
总 Rg total_rg	54.97 Å
总原子数 total_atoms	15629
残基数 n_residues	1972
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	181.9 Å
Rg (实空间) rg_real	54.98 Å
Rg 误差 (实空间) rg_real_error	2.20 Å
I(0) (实空间) i0_real	7.1880e+08
I(0) 误差 (实空间) i0_real_error	1.6320e+07
Rg (倒空间) rg_reciprocal	53.67 Å
I(0) (倒空间) i0_reciprocal	717400000.0000
解质量估计 total_estimate	0.5027
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	37.6 Å
偏度 Skewness skewness	0.603
峰度 Kurtosis kurtosis	-0.444
角度范围 angular_range	— – 0.1450 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	136600000.0000
实空间数据点数 n_real_points	30
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.579; Stabil: 1.000; Sysdev: 0.017; Positv: 1.000; Valcen: 0.685; Smooth: 0.057

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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) 9 domains

CATH v4.4 (9 domains)

结构域编号 domain_id	2jl9A02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	490 — Globin-like
同源超家族 H-superfamily homologous superfamily	60 — Phage p2 RNA dependent RNA polymerase domain

结构域编号 domain_id	2jl9A03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	1600 —

结构域编号 domain_id	2jl9A04
类 Class class	6 — Special
架构 Architecture architecture	20 — Other non-globular
拓扑 Topology topology	410 — Dihydrolipoamide Transferase
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	2jl9B02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	490 — Globin-like
同源超家族 H-superfamily homologous superfamily	60 — Phage p2 RNA dependent RNA polymerase domain

结构域编号 domain_id	2jl9B03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	1600 —

结构域编号 domain_id	2jl9B04
类 Class class	6 — Special
架构 Architecture architecture	20 — Other non-globular
拓扑 Topology topology	410 — Dihydrolipoamide Transferase
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	2jl9C02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	490 — Globin-like
同源超家族 H-superfamily homologous superfamily	60 — Phage p2 RNA dependent RNA polymerase domain

结构域编号 domain_id	2jl9C03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	1600 —

结构域编号 domain_id	2jl9C04
类 Class class	6 — Special
架构 Architecture architecture	20 — Other non-globular
拓扑 Topology topology	410 — Dihydrolipoamide Transferase
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	106.519 Å
晶胞边长 b length_b	91.599 Å
晶胞边长 c length_c	142.705 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	101.64 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	6

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	3.200 Å
最低分辨率 resolution_low	19.915 Å
R 因子 r_factor	0.2177
R_work r_work	0.2148
R_free r_free	0.2720

描述 description	RNA-DIRECTED RNA POLYMERASE
分子量 formula_weight	75033.4 kDa
EC 编号 ec_number	2.7.7.48
突变 mutation	YES
来源方法 src_method	man
拷贝数 entity_count	3

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C
原子数 atom_count	15629

Structural explanation for the role of Mn in the activity of phi6 RNA- dependent RNA polymerase

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) 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	PSEUDOMONAS PHAGE PHI6
NCBI 分类编号 ncbi_taxonomy_id	10879
宿主生物 host_organism	ESCHERICHIA COLI

fit	/app/data/saxs_computation/jl/2jl9/2jl9.fit
pddf	/app/data/pr_computation/jl/2jl9/2jl9.pr.out
profile	/app/data/saxs_computation/jl/2jl9/2jl9.dat