SAXSdb — 2jlf

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2jlf
沉积日期 deposition_date	2008-09-08
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	55.33 Å
回转半径 Rg (电子) rg_electron	56.11 Å
零角强度 I(0) i0	714452000.00
分子量 molecular_weight	221820.0 kDa
排除体积 excluded_volume	277180 Å³
包络体积 envelope_volume	387810 Å³
水化壳体积 shell_volume	63704 Å³
包络直径 envelope_diameter	190.7 Å
壳层 Rg shell_rg	50.84 Å
包络 Rg envelope_rg	54.42 Å
形状 Rg shape_rg	56.09 Å
总 Rg total_rg	56.02 Å
总原子数 total_atoms	15610
残基数 n_residues	1969
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	179.6 Å
Rg (实空间) rg_real	55.89 Å
Rg 误差 (实空间) rg_real_error	1.97 Å
I(0) (实空间) i0_real	7.1440e+08
I(0) 误差 (实空间) i0_real_error	1.4760e+07
Rg (倒空间) rg_reciprocal	54.83 Å
I(0) (倒空间) i0_reciprocal	713300000.0000
解质量估计 total_estimate	0.7499
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	38.5 Å
偏度 Skewness skewness	0.486
峰度 Kurtosis kurtosis	-0.561
角度范围 angular_range	— – 0.1400 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	118300000.0000
实空间数据点数 n_real_points	29
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.679; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.692; Smooth: 0.017

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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)

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	15610

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 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	2

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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	2jlfA02
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	2jlfA03
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	2jlfA04
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	2jlfB02
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	2jlfB03
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	2jlfB04
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	2jlfC02
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	2jlfC03
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	2jlfC04
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	110.040 Å
晶胞边长 b length_b	110.040 Å
晶胞边长 c length_c	159.132 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	3.200 Å
最低分辨率 resolution_low	18.021 Å
R 因子 r_factor	0.2304
R_work r_work	0.2275
R_free r_free	0.2860

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