SAXSdb — 2ga9

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2ga9
沉积日期 deposition_date	2006-03-08
结构标题 title	Crystal Structure of the Heterodimeric Vaccinia Virus Polyadenylate Polymerase with Bound ATP-gamma-S
关键词 keywords	polyadenylate polymerase, nucleotidyltransferase, poxvirus, heterodimer, processivity, 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	29.13 Å
回转半径 Rg (电子) rg_electron	28.09 Å
零角强度 I(0) i0	114483000.00
分子量 molecular_weight	86553.0 kDa
排除体积 excluded_volume	109240 Å³
包络体积 envelope_volume	130720 Å³
水化壳体积 shell_volume	38069 Å³
包络直径 envelope_diameter	90.7 Å
壳层 Rg shell_rg	36.16 Å
包络 Rg envelope_rg	28.12 Å
形状 Rg shape_rg	28.08 Å
总 Rg total_rg	28.89 Å
总原子数 total_atoms	6073
残基数 n_residues	733
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	86.7 Å
Rg (实空间) rg_real	29.02 Å
Rg 误差 (实空间) rg_real_error	0.55 Å
I(0) (实空间) i0_real	1.1450e+08
I(0) 误差 (实空间) i0_real_error	1.6050e+06
Rg (倒空间) rg_reciprocal	29.06 Å
I(0) (倒空间) i0_reciprocal	114500000.0000
解质量估计 total_estimate	0.9109
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	32.1 Å
偏度 Skewness skewness	0.183
峰度 Kurtosis kurtosis	-0.597
角度范围 angular_range	— – 0.2700 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	36610000.0000
实空间数据点数 n_real_points	55
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.977; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.917

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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 (5)

Entity 1 polymer

描述 description	;Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase ;
分子量 formula_weight	34589.0 kDa
EC 编号 ec_number	2.1.1.57
突变 mutation	R140A K142A R143A
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	6333

MDVVSLDKPFMYFEEIDNELDYEPESANEVAKKLPYQGQLKLLLGELFFLSKLQRHGILDGATVVYIGSAPGTHIRYLRDHFYNLGVIIKWMLIDGRHHDPILNGLRDVTLVTRFVDEEYLRSIKKQLHPSKIILISDVASAAGGNEPSTADLLSNYALQNVMISILNPVASSLKWRCPFPDQWIKDFYIPHGNKMLQPFAPSYSAEMRLLSIYTGENMRLTRVTKSDAVNYEKKMYYLNKIVRNKVVVNFDYPNQEYDYFHMYFMLRTVYCNKTFPTTKAKVLFLQQSIFRFLNIP

来源 Source

来源生物 organism	Vaccinia virus
NCBI 分类编号 ncbi_taxonomy_id	10245
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

描述 description	Poly(A) polymerase catalytic subunit
分子量 formula_weight	54388.8 kDa
EC 编号 ec_number	2.7.7.19
突变 mutation	L36S
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	D

PNITLKIIETYLGRVPSVNEYHMLKSQARNIQKITVFNKDIFVSLVKKNKKRFFSDVNTSASEIKDRILSYFSKQTQTYNIGKLFTIIELQSVLVTTYTDILGVLTIKAPNVISSKISYNVTSMEELARDMLNSMNVAVIDKAKVMGRHNVSSLVKNVNKLMEEYLRRHNKSCICYGSYSLYLINPNIRYGDIDILQTNSRTFLIDLAFLIKFITGNNIILSKIPYLRNYMVIKDENDNHIIDSFNIRQDTMNVVPKIFIDNIYIVDPTFQLLNMIKMFSQIDRLEDLSKDPEKFNARMATMLEYVRYTHGIVFDGKRNNMPMKCIIDENNRIVTVTTKDYFSFKKCLVYLDENVLSSDILDLNADTSCDFESVTNSVYLIHDNIMYTYFSNTILLSDKGKVHEISARGLCAHILLYQMLTSGEYKQCLSDLLNSMMNRDKIPIYSHTERDKKPGRHGFINIEKDIIVF

来源 Source

来源生物 organism	Vaccinia virus
NCBI 分类编号 ncbi_taxonomy_id	10245
宿主生物 host_organism	Escherichia coli

Entity 3 non-polymer

描述 description	CALCIUM ION
分子量 formula_weight	40.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 non-polymer

描述 description	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
分子量 formula_weight	523.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 5 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	260

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6. 折叠分类 (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d2ga9a_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
超家族 Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
家族 Family family	c.66.1.25 — mRNA cap methylase

结构域编号 domain_id	d2ga9d1
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.69 — Poly(A) polymerase catalytic subunit-like
超家族 Superfamily superfamily	e.69.1 — Poly(A) polymerase catalytic subunit-like
家族 Family family	e.69.1.1 — Poxvirus poly(A) polymerase catalytic subunit-like

CATH v4.4 (3 domains)

结构域编号 domain_id	2ga9A00
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	150 — Vaccinia Virus protein VP39

结构域编号 domain_id	2ga9D01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
同源超家族 H-superfamily homologous superfamily	320 — Poxvirus poly(A) polymerase, N domain

结构域编号 domain_id	2ga9D03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	460 — Beta Polymerase; domain 2
同源超家族 H-superfamily homologous superfamily	60 — Poxvirus poly(A) polymerase, nucleotidyltransferase domain

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7. 引用文献 (1)

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晶胞边长 a length_a	70.050 Å
晶胞边长 b length_b	91.690 Å
晶胞边长 c length_c	133.700 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	90.00 °
晶胞分子数 Z z_pdb	4

空间群 space_group	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	2.300 Å
最低分辨率 resolution_low	50.000 Å
R 因子 r_factor	0.2250
R_work r_work	0.2220
R_free r_free	0.2600

fit	/app/data/saxs_computation/ga/2ga9/2ga9.fit
pddf	/app/data/pr_computation/ga/2ga9/2ga9.pr.out
profile	/app/data/saxs_computation/ga/2ga9/2ga9.dat

Crystal Structure of the Heterodimeric Vaccinia Virus Polyadenylate Polymerase with Bound ATP-gamma-S

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 (5)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 water

6. 折叠分类 (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)