SAXSdb — 2jlg

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2jlg
沉积日期 deposition_date	2008-09-09
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	;NUCLEOTIDYLTRANSFERASE, RNA-DIRECTED RNA POLYMERASE, METAL-BINDING, RNA POLYMERASE, RNA REPLICATION, VIRION, MANGANESE, MAGNESIUM, TRANSFERASE, VIRAL POLYMERASE, NUCLEOTIDE-BINDING ;; 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	54.61 Å
回转半径 Rg (电子) rg_electron	55.40 Å
零角强度 I(0) i0	795427000.00
分子量 molecular_weight	229260.0 kDa
排除体积 excluded_volume	284450 Å³
包络体积 envelope_volume	387190 Å³
水化壳体积 shell_volume	64051 Å³
包络直径 envelope_diameter	189.4 Å
壳层 Rg shell_rg	50.53 Å
包络 Rg envelope_rg	53.98 Å
形状 Rg shape_rg	55.38 Å
总 Rg total_rg	55.32 Å
总原子数 total_atoms	16099
残基数 n_residues	1993
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	177.8 Å
Rg (实空间) rg_real	55.14 Å
Rg 误差 (实空间) rg_real_error	2.19 Å
I(0) (实空间) i0_real	7.9540e+08
I(0) 误差 (实空间) i0_real_error	1.6750e+07
Rg (倒空间) rg_reciprocal	54.13 Å
I(0) (倒空间) i0_reciprocal	794200000.0000
解质量估计 total_estimate	0.7497
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	3
主峰位置 r_peak_primary	36.8 Å
偏度 Skewness skewness	0.481
峰度 Kurtosis kurtosis	-0.572
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	127000000.0000
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: 0.670; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.708; Smooth: 0.023

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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	RNA-DIRECTED RNA POLYMERASE
分子量 formula_weight	74902.2 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 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C
原子数 atom_count	16099

PRRAPAFPLSDIKAQMLFANNIKAQQASKRSFKEGAIETYEGLLSVDPRFLSFKNELSRYLTDHFPANVDEYGRVYGNGVRTNFFGMRHMNGFPMIPATWPLASNLKKRADADLADGPVSERDNLLFRAAVRLMFSDLEPVPLKIRKGSSTCIPYFSNDMGTKIEIAERALEKAEEAGNLMLQGKFDDAYQLHQMGGAYYVVYRAQSTDAITLDPKTGKFVSKDRMVADFEYAVTGGEQGSLFAASKDASRLKEQYGIDVPDGFFCERRRTAMGGPFALNAPIMAVAQPVRNKIYSKYAYTFHHTTRLNKEEKVKEWSLCVATDVSDHDTFWPGWLRDLICDELLNMGYAPWWVKLFETSLKLPVYVGAPAPEQGHTLLGDPSNPDLEVGLSSGQGATDLMGTLLMSITYLVMQLDHTAPHLNSRIKDMPSACRFLDSYWQGHEEIRQISKSDDAMLGWTKGRALVGGHRLFEMLKEGKVNPSPYMKISYQHGGAFLGDILLYDSRREPGSAIFVGNINSMLNNQFSPEYGVQSGVRDRSKRKRPFPGLAWASMKDTYGACPIYSDVLEAIERCWWNAFGESYRAYREDMLKRDTLELSRYVASMARQAGLAELTPIDLEVLADPNKLQYKWTEADVSANIHEVLMHGVSVEKTERFLRSVMPR

来源 Source

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

Entity 2 polymer

描述 description	;5'-D(*DT DT DT DC DCP)-3' ;
分子量 formula_weight	1446.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polydeoxyribonucleotide
链编号 strand_id	D,E,F

TTTCC

Entity 3 non-polymer

描述 description	GUANOSINE-5'-TRIPHOSPHATE
分子量 formula_weight	523.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 4 non-polymer

描述 description	MANGANESE (II) ION
分子量 formula_weight	54.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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6. 折叠分类 (SCOP + CATH) 12 domains

SCOP 2.08 (3 domains)

结构域编号 domain_id	d2jlga_
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.8 — DNA/RNA polymerases
超家族 Superfamily superfamily	e.8.1 — DNA/RNA polymerases
家族 Family family	e.8.1.6 — dsRNA phage RNA-dependent RNA-polymerase

结构域编号 domain_id	d2jlgb_
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.8 — DNA/RNA polymerases
超家族 Superfamily superfamily	e.8.1 — DNA/RNA polymerases
家族 Family family	e.8.1.6 — dsRNA phage RNA-dependent RNA-polymerase

结构域编号 domain_id	d2jlgc_
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.8 — DNA/RNA polymerases
超家族 Superfamily superfamily	e.8.1 — DNA/RNA polymerases
家族 Family family	e.8.1.6 — dsRNA phage RNA-dependent RNA-polymerase

CATH v4.4 (9 domains)

结构域编号 domain_id	2jlgA02
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	2jlgA03
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	2jlgA04
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	2jlgB02
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	2jlgB03
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	2jlgB04
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	2jlgC02
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	2jlgC03
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	2jlgC04
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	109.026 Å
晶胞边长 b length_b	109.026 Å
晶胞边长 c length_c	158.835 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	120.00 °
晶胞分子数 Z z_pdb	9

空间群 space_group	P 32
空间群编号 int_tables_number	145
晶系 crystal_system	—

分辨率 resolution	2.800 Å
最低分辨率 resolution_low	19.944 Å
R 因子 r_factor	0.2196
R_work r_work	0.2156
R_free r_free	0.2947

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

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 (4)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

Entity 3 non-polymer

Entity 4 non-polymer

6. 折叠分类 (SCOP + CATH) 12 domains

SCOP 2.08 (3 domains)

CATH v4.4 (9 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)