SAXSdb — 1uvl

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1uvl
沉积日期 deposition_date	2004-01-21
结构标题 title	The structural basis for RNA specificity and Ca2 inhibition of an RNA-dependent RNA polymerase phi6p2 with 5nt RNA. Conformation B
关键词 keywords	POLYMERASE, TRANSFERASE, OLIGONUCLEOTIDE POLYMERASE, TRANSCRIPTION, STRUCTURAL PROTEIN; 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	53.57 Å
回转半径 Rg (电子) rg_electron	54.53 Å
零角强度 I(0) i0	784936000.00
分子量 molecular_weight	228990.0 kDa
排除体积 excluded_volume	284720 Å³
包络体积 envelope_volume	377220 Å³
水化壳体积 shell_volume	64467 Å³
包络直径 envelope_diameter	192.2 Å
壳层 Rg shell_rg	48.84 Å
包络 Rg envelope_rg	53.82 Å
形状 Rg shape_rg	54.53 Å
总 Rg total_rg	54.34 Å
总原子数 total_atoms	16089
残基数 n_residues	2007
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	180.0 Å
Rg (实空间) rg_real	54.25 Å
Rg 误差 (实空间) rg_real_error	2.18 Å
I(0) (实空间) i0_real	7.8490e+08
I(0) 误差 (实空间) i0_real_error	1.5360e+07
Rg (倒空间) rg_reciprocal	52.99 Å
I(0) (倒空间) i0_reciprocal	783500000.0000
解质量估计 total_estimate	0.7267
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	37.2 Å
偏度 Skewness skewness	0.600
峰度 Kurtosis kurtosis	-0.454
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	120100000.0000
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: 0.572; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.658; Smooth: 0.071

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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 (3)

Entity 1 polymer

描述 description	RNA-directed RNA polymerase
分子量 formula_weight	74903.2 kDa
EC 编号 ec_number	2.7.7.48
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,C,E
原子数 atom_count	16089

PRRAPAFPLSDIKAQMLFANNIKAQQASKRSFKEGAIETYEGLLSVDPRFLSFKNELSRYLTDHFPANVDEYGRVYGNGVRTNFFGMRHMNGFPMIPATWPLASNLKKRADADLADGPVSERDNLLFRAAVRLMFSDLEPVPLKIRKGSSTCIPYFSNDMGTKIEIAERALEKAEEAGNLMLQGKFDDAYQLHQMGGAYYVVYRAQSTDAITLDPKTGKFVSKDRMVADFEYAVTGGEQGSLFAASKDASRLKEQYGIDVPDGFFCERRRTAMGGPFALNAPIMAVAQPVRNKIYSKYAYTFHHTTRLNKEEKVKEWSLCVATDVSDHDTFWPGWLRDLICDELLNMGYAPWWVKLFETSLKLPVYVGAPAPEQGHTLLGDPSNPDLEVGLSSGQGATDLMGTLLMSITYLVMQLDHTAPHLNSRIKDMPSACRFLDSYWQGHEEIRQISKSDDAMLGWTKGRALVGGHRLFEMLKEGKVNPSPYMKISYEHGGAFLGDILLYDSRREPGSAIFVGNINSMLNNQFSPEYGVQSGVRDRSKRKRPFPGLAWASMKDTYGACPIYSDVLEAIERCWWNAFGESYRAYREDMLKRDTLELSRYVASMARQAGLAELTPIDLEVLADPNKLQYKWTEADVSANIHEVLMHGVSVEKTERFLRSVMPR

来源 Source

来源生物 organism	Pseudomonas phage phi6
通用名 common_name	Bacteriophage phi-6
NCBI 分类编号 ncbi_taxonomy_id	10879
宿主生物 host_organism	Escherichia coli

Entity 2 polymer

描述 description	5'-R(UPUPUPCP*CP)-3'
分子量 formula_weight	1483.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	B,D,F

UUUCC

Entity 3 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	3

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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	d1uvla_
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	d1uvlc_
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	d1uvle_
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	1uvlA02
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	1uvlA03
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	1uvlA04
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	1uvlC02
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	1uvlC03
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	1uvlC04
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	1uvlE02
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	1uvlE03
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	1uvlE04
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	105.946 Å
晶胞边长 b length_b	91.881 Å
晶胞边长 c length_c	140.762 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	101.56 °
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	2.000 Å
最低分辨率 resolution_low	19.820 Å
R 因子 r_factor	0.2810
R_work r_work	0.2810
R_free r_free	0.2990

fit	/app/data/saxs_computation/uv/1uvl/1uvl.fit
pddf	/app/data/pr_computation/uv/1uvl/1uvl.pr.out
profile	/app/data/saxs_computation/uv/1uvl/1uvl.dat

The structural basis for RNA specificity and Ca2 inhibition of an RNA-dependent RNA polymerase phi6p2 with 5nt RNA. Conformation B

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 (3)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

Entity 3 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)