1q57

The Crystal Structure of the Bifunctional Primase-Helicase of Bacteriophage T7

Method: X-RAY DIFFRACTION D_max: 162.2 Å Quality: GOOD

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	1q57
沉积日期 deposition_date	2003-08-06
结构标题 title	The Crystal Structure of the Bifunctional Primase-Helicase of Bacteriophage T7
关键词 keywords	primase, helicase, dNTPase, DNA replication, TRANSFERASE; 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	54.51 Å
回转半径 Rg (电子) rg_electron	53.74 Å
零角强度 I(0) i0	2086230000.00
分子量 molecular_weight	373720.0 kDa
排除体积 excluded_volume	464180 Å³
包络体积 envelope_volume	723850 Å³
水化壳体积 shell_volume	109180 Å³
包络直径 envelope_diameter	156.6 Å
壳层 Rg shell_rg	61.99 Å
包络 Rg envelope_rg	50.69 Å
形状 Rg shape_rg	53.78 Å
总 Rg total_rg	53.84 Å
总原子数 total_atoms	26208
残基数 n_residues	3381
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	162.2 Å
Rg (实空间) rg_real	54.16 Å
Rg 误差 (实空间) rg_real_error	0.81 Å
I(0) (实空间) i0_real	2.0860e+09
I(0) 误差 (实空间) i0_real_error	3.3890e+07
Rg (倒空间) rg_reciprocal	54.78 Å
I(0) (倒空间) i0_reciprocal	2088000000.0000
解质量估计 total_estimate	0.8348
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	72.7 Å
偏度 Skewness skewness	-0.068
峰度 Kurtosis kurtosis	-0.677
角度范围 angular_range	— – 0.1450 Å⁻¹
当前正则化参数 α current_alpha	0.0002
最高正则化参数 α highest_alpha	87290000.0000
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: 0.960; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.968; Smooth: 0.000

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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) 23 domains

SCOP 2.08 (14 domains)

结构域编号 domain_id	d1q57a1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family family	c.37.1.11 — RecA protein-like (ATPase-domain)

结构域编号 domain_id	d1q57a2
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.13 — DNA primase core
超家族 Superfamily superfamily	e.13.1 — DNA primase core
家族 Family family	e.13.1.2 — Primase fragment of primase-helicase protein

结构域编号 domain_id	d1q57b1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family family	c.37.1.11 — RecA protein-like (ATPase-domain)

结构域编号 domain_id	d1q57b2
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.13 — DNA primase core
超家族 Superfamily superfamily	e.13.1 — DNA primase core
家族 Family family	e.13.1.2 — Primase fragment of primase-helicase protein

结构域编号 domain_id	d1q57c1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family family	c.37.1.11 — RecA protein-like (ATPase-domain)

结构域编号 domain_id	d1q57c2
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.13 — DNA primase core
超家族 Superfamily superfamily	e.13.1 — DNA primase core
家族 Family family	e.13.1.2 — Primase fragment of primase-helicase protein

结构域编号 domain_id	d1q57d1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family family	c.37.1.11 — RecA protein-like (ATPase-domain)

结构域编号 domain_id	d1q57d2
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.13 — DNA primase core
超家族 Superfamily superfamily	e.13.1 — DNA primase core
家族 Family family	e.13.1.2 — Primase fragment of primase-helicase protein

结构域编号 domain_id	d1q57e1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family family	c.37.1.11 — RecA protein-like (ATPase-domain)

结构域编号 domain_id	d1q57e2
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.13 — DNA primase core
超家族 Superfamily superfamily	e.13.1 — DNA primase core
家族 Family family	e.13.1.2 — Primase fragment of primase-helicase protein

结构域编号 domain_id	d1q57f1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family family	c.37.1.11 — RecA protein-like (ATPase-domain)

结构域编号 domain_id	d1q57f2
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.13 — DNA primase core
超家族 Superfamily superfamily	e.13.1 — DNA primase core
家族 Family family	e.13.1.2 — Primase fragment of primase-helicase protein

结构域编号 domain_id	d1q57g1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family family	c.37.1.11 — RecA protein-like (ATPase-domain)

结构域编号 domain_id	d1q57g2
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.13 — DNA primase core
超家族 Superfamily superfamily	e.13.1 — DNA primase core
家族 Family family	e.13.1.2 — Primase fragment of primase-helicase protein

CATH v4.4 (9 domains)

结构域编号 domain_id	1q57A02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

结构域编号 domain_id	1q57B02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

结构域编号 domain_id	1q57C02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

结构域编号 domain_id	1q57D02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

结构域编号 domain_id	1q57E02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

结构域编号 domain_id	1q57F02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

结构域编号 domain_id	1q57G01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	20 — Single Sheet
拓扑 Topology topology	25 — N-terminal domain of TfIIb
同源超家族 H-superfamily homologous superfamily	180 —

结构域编号 domain_id	1q57G02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1360 — Dna Topoisomerase Vi A Subunit; Chain: A, domain 2
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1q57G03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

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7. 引用文献 (1)

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晶胞边长 a length_a	117.179 Å
晶胞边长 b length_b	171.567 Å
晶胞边长 c length_c	118.581 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	99.86 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	14

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	3.450 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.3008
R_work r_work	0.2994
R_free r_free	0.3260

描述 description	DNA primase/helicase
分子量 formula_weight	55857.0 kDa
EC 编号 ec_number	2.7.7.-
突变 mutation	G317V, K318M
来源方法 src_method	man
拷贝数 entity_count	7

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F,G
原子数 atom_count	26208

The Crystal Structure of the Bifunctional Primase-Helicase of Bacteriophage T7

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) 23 domains

SCOP 2.08 (14 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	Enterobacteria phage T7
NCBI 分类编号 ncbi_taxonomy_id	10760
宿主生物 host_organism	Escherichia coli

fit	/app/data/saxs_computation/q5/1q57/1q57.fit
pddf	/app/data/pr_computation/q5/1q57/1q57.pr.out
profile	/app/data/saxs_computation/q5/1q57/1q57.dat