SAXSdb — 1wac

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1wac
沉积日期 deposition_date	2004-10-26
结构标题 title	Back-priming mode of Phi6 RNA-dependent RNA polymerase
关键词 keywords	POLYMERASE, PHI6 RNA-DEPENDENT RNA POLYMERASE, TRANSCRIPTION; POLYMERASE
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	52.22 Å
回转半径 Rg (电子) rg_electron	52.68 Å
零角强度 I(0) i0	731153000.00
分子量 molecular_weight	223030.0 kDa
排除体积 excluded_volume	278400 Å³
包络体积 envelope_volume	381570 Å³
水化壳体积 shell_volume	65404 Å³
包络直径 envelope_diameter	184.1 Å
壳层 Rg shell_rg	49.79 Å
包络 Rg envelope_rg	51.68 Å
形状 Rg shape_rg	52.69 Å
总 Rg total_rg	52.55 Å
总原子数 total_atoms	15693
残基数 n_residues	1986
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	171.0 Å
Rg (实空间) rg_real	52.66 Å
Rg 误差 (实空间) rg_real_error	1.85 Å
I(0) (实空间) i0_real	7.3120e+08
I(0) 误差 (实空间) i0_real_error	1.5170e+07
Rg (倒空间) rg_reciprocal	51.83 Å
I(0) (倒空间) i0_reciprocal	730300000.0000
解质量估计 total_estimate	0.7887
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	39.9 Å
偏度 Skewness skewness	0.526
峰度 Kurtosis kurtosis	-0.457
角度范围 angular_range	— – 0.1500 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	113800000.0000
实空间数据点数 n_real_points	31
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.766; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.885; Smooth: 0.067

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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) 12 domains

SCOP 2.08 (3 domains)

结构域编号 domain_id	d1waca_
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	d1wacb_
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	d1wacc_
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	1wacA02
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	1wacA03
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	1wacA04
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	1wacB02
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	1wacB03
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	1wacB04
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	1wacC02
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	1wacC03
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	1wacC04
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	76.579 Å
晶胞边长 b length_b	105.851 Å
晶胞边长 c length_c	157.712 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	98.86 °
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	3.000 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.2410
R_work r_work	0.2410
R_free r_free	0.2800

描述 description	P2 PROTEIN
分子量 formula_weight	74440.6 kDa
突变 mutation	YES
来源方法 src_method	man
拷贝数 entity_count	3

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C
原子数 atom_count	15693

Back-priming mode 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 (1)

Entity 1 polymer

聚合体 Polymer

来源 Source

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)

来源生物 organism	PSEUDOMONAS PHAGE PHI-6
NCBI 分类编号 ncbi_taxonomy_id	10879
宿主生物 host_organism	ESCHERICHIA COLI

fit	/app/data/saxs_computation/wa/1wac/1wac.fit
pddf	/app/data/pr_computation/wa/1wac/1wac.pr.out
profile	/app/data/saxs_computation/wa/1wac/1wac.dat