1s4f

Crystal Structure of RNA-dependent RNA polymerase construct 2 from bovine viral diarrhea virus (BVDV)

Method: X-RAY DIFFRACTION D_max: 198.5 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	1s4f
沉积日期 deposition_date	2004-01-16
结构标题 title	Crystal Structure of RNA-dependent RNA polymerase construct 2 from bovine viral diarrhea virus (BVDV)
关键词 keywords	;Polymerase, RNA synthesis, primer independent initiation, de novo initiation, bovine viral diarrhea virus, BVDV, REPLICATION, RNA BINDING PROTEIN ;; REPLICATION, RNA BINDING PROTEIN
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	63.52 Å
回转半径 Rg (电子) rg_electron	64.83 Å
零角强度 I(0) i0	976928000.00
分子量 molecular_weight	265520.0 kDa
排除体积 excluded_volume	333930 Å³
包络体积 envelope_volume	489480 Å³
水化壳体积 shell_volume	67587 Å³
包络直径 envelope_diameter	216.8 Å
壳层 Rg shell_rg	57.01 Å
包络 Rg envelope_rg	63.43 Å
形状 Rg shape_rg	64.83 Å
总 Rg total_rg	64.63 Å
总原子数 total_atoms	18714
残基数 n_residues	2322
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	198.5 Å
Rg (实空间) rg_real	64.52 Å
Rg 误差 (实空间) rg_real_error	1.76 Å
I(0) (实空间) i0_real	9.7680e+08
I(0) 误差 (实空间) i0_real_error	1.7970e+07
Rg (倒空间) rg_reciprocal	62.55 Å
I(0) (倒空间) i0_reciprocal	973500000.0000
解质量估计 total_estimate	0.5300
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	39.7 Å
偏度 Skewness skewness	0.470
峰度 Kurtosis kurtosis	-0.743
角度范围 angular_range	— – 0.1250 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	40500000.0000
实空间数据点数 n_real_points	26
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.720; Stabil: 0.999; Sysdev: 0.004; Positv: 1.000; Valcen: 0.710; Smooth: 0.005

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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) 8 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1s4fa_
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.8.1.4 — RNA-dependent RNA-polymerase

结构域编号 domain_id	d1s4fb_
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.8.1.4 — RNA-dependent RNA-polymerase

结构域编号 domain_id	d1s4fc_
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.8.1.4 — RNA-dependent RNA-polymerase

结构域编号 domain_id	d1s4fd_
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.8.1.4 — RNA-dependent RNA-polymerase

CATH v4.4 (4 domains)

结构域编号 domain_id	1s4fA04
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	270 — Reverse transcriptase/Diguanylate cyclase domain

结构域编号 domain_id	1s4fB04
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	270 — Reverse transcriptase/Diguanylate cyclase domain

结构域编号 domain_id	1s4fC04
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	270 — Reverse transcriptase/Diguanylate cyclase domain

结构域编号 domain_id	1s4fD04
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	270 — Reverse transcriptase/Diguanylate cyclase domain

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7. 引用文献 (1)

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晶胞边长 a length_a	412.271 Å
晶胞边长 b length_b	412.271 Å
晶胞边长 c length_c	95.574 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	48

空间群 space_group	P 62 2 2
空间群编号 int_tables_number	180
晶系 crystal_system	—

分辨率 resolution	3.000 Å
最低分辨率 resolution_low	29.690 Å
R 因子 r_factor	0.2540
R_work r_work	0.2540
R_free r_free	0.3030

描述 description	RNA-dependent RNA polymerase
分子量 formula_weight	68946.8 kDa
来源方法 src_method	man
拷贝数 entity_count	4

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	18714

Crystal Structure of RNA-dependent RNA polymerase construct 2 from bovine viral diarrhea virus (BVDV)

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

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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)

来源生物 organism	Bovine viral diarrhea virus 1
NCBI 分类编号 ncbi_taxonomy_id	11099
宿主生物 host_organism	Escherichia coli

fit	/app/data/saxs_computation/s4/1s4f/1s4f.fit
pddf	/app/data/pr_computation/s4/1s4f/1s4f.pr.out
profile	/app/data/saxs_computation/s4/1s4f/1s4f.dat