SAXSdb — 1tp7

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1tp7
沉积日期 deposition_date	2004-06-15
结构标题 title	Crystal Structure of the RNA-dependent RNA Polymerase from Human Rhinovirus 16
关键词 keywords	Rhinovirus, RNA, polymerase, 3D, TRANSFERASE; TRANSFERASE
实验方法 method	X-RAY DIFFRACTION

▼

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	48.59 Å
回转半径 Rg (电子) rg_electron	48.74 Å
零角强度 I(0) i0	619041000.00
分子量 molecular_weight	211650.0 kDa
排除体积 excluded_volume	266510 Å³
包络体积 envelope_volume	377800 Å³
水化壳体积 shell_volume	66597 Å³
包络直径 envelope_diameter	174.9 Å
壳层 Rg shell_rg	50.23 Å
包络 Rg envelope_rg	47.51 Å
形状 Rg shape_rg	48.76 Å
总 Rg total_rg	48.77 Å
总原子数 total_atoms	14781
残基数 n_residues	1800
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

▼

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	165.8 Å
Rg (实空间) rg_real	48.76 Å
Rg 误差 (实空间) rg_real_error	1.90 Å
I(0) (实空间) i0_real	6.1900e+08
I(0) 误差 (实空间) i0_real_error	1.3200e+07
Rg (倒空间) rg_reciprocal	48.59 Å
I(0) (倒空间) i0_reciprocal	618900000.0000
解质量估计 total_estimate	0.8443
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	67.3 Å
偏度 Skewness skewness	0.372
峰度 Kurtosis kurtosis	-0.306
角度范围 angular_range	— – 0.1600 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	105600000.0000
实空间数据点数 n_real_points	33
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.831; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.968; Smooth: 0.512

▶

4. 晶体学与实验 4. Crystallography & Experiment

▶

5. 实体与聚合体信息 (4)

Entity 1 polymer

描述 description	Genome polyprotein
分子量 formula_weight	52813.0 kDa
EC 编号 ec_number	2.7.7.48
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	15051

GQIQISKHVKDVGLPSIHTPTKTKLQPSVFYDIFPGSKEPAVLTEKDPRLKVDFDSALFSKYKGNTECSLNEHIQVAVAHYSAQLATLDIDPQPIAMEDSVFGMDGLEALDLNTSAGYPYVTLGIKKKDLINNKTKDISKLKLALDKYDVDLPMITFLKDELRKKDKIAAGKTRVIEASSINDTILFRTVYGNLFSKFHLNPGVVTGCAVGCDPETFWSKIPLMLDGDCIMAFDYTNYDGSIHPIWFKALGMVLDNLSFNPTLINRLCNSKHIFKSTYYEVEGGVPSGCSGTSIFNSMINNIIIRTLVLDAYKHIDLDKLKIIAYGDDVIFSYKYKLDMEAIAKEGQKYGLTITPADKSSEFKELDYGNVTFLKRGFRQDDKYKFLIHPTFPVEEIYESIRWTKKPSQMQEHVLSLCHLMWHNGPEIYKDFETKIRSVSAGRALYIPPYELLRHEWYEKF

来源 Source

来源生物 organism	Human rhinovirus 16
NCBI 分类编号 ncbi_taxonomy_id	31708
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

描述 description	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 3 non-polymer

描述 description	3-[BENZYL(DIMETHYL)AMMONIO]PROPANE-1-SULFONATE
分子量 formula_weight	257.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 4 water

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	270

▼

6. 折叠分类 (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1tp7a_
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	d1tp7b_
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	d1tp7c_
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	d1tp7d_
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 (8 domains)

结构域编号 domain_id	1tp7A02
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	1tp7A03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	960 — Mitochondrial Import Receptor Subunit Tom20; Chain A
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	1tp7B02
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	1tp7B03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	960 — Mitochondrial Import Receptor Subunit Tom20; Chain A
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	1tp7C02
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	1tp7C03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	960 — Mitochondrial Import Receptor Subunit Tom20; Chain A
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	1tp7D02
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	1tp7D03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	960 — Mitochondrial Import Receptor Subunit Tom20; Chain A
同源超家族 H-superfamily homologous superfamily	20 —

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	59.428 Å
晶胞边长 b length_b	118.890 Å
晶胞边长 c length_c	183.107 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	96.06 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

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	2.400 Å
最低分辨率 resolution_low	50.000 Å
R 因子 r_factor	0.2430
R_work r_work	0.2430
R_free r_free	0.2920

fit	/app/data/saxs_computation/tp/1tp7/1tp7.fit
pddf	/app/data/pr_computation/tp/1tp7/1tp7.pr.out
profile	/app/data/saxs_computation/tp/1tp7/1tp7.dat

Crystal Structure of the RNA-dependent RNA Polymerase from Human Rhinovirus 16

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