1gs0

Crystal structure of the catalytic fragment of murine poly(ADP-ribose) polymerase-2

Method: X-RAY DIFFRACTION D_max: 106.9 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	1gs0
沉积日期 deposition_date	2001-12-19
结构标题 title	Crystal structure of the catalytic fragment of murine poly(ADP-ribose) polymerase-2
关键词 keywords	TRANSFERASE, CATALYTIC FRAGMENT, POLYMERASE TRANSFERASE, NUCLEAR PROTEIN, DNA-BINDING; 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	33.94 Å
回转半径 Rg (电子) rg_electron	33.40 Å
零角强度 I(0) i0	92412600.00
分子量 molecular_weight	77733.0 kDa
排除体积 excluded_volume	97876 Å³
包络体积 envelope_volume	128560 Å³
水化壳体积 shell_volume	32779 Å³
包络直径 envelope_diameter	111.4 Å
壳层 Rg shell_rg	39.15 Å
包络 Rg envelope_rg	32.83 Å
形状 Rg shape_rg	33.39 Å
总 Rg total_rg	33.91 Å
总原子数 total_atoms	5461
残基数 n_residues	688
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	106.9 Å
Rg (实空间) rg_real	34.04 Å
Rg 误差 (实空间) rg_real_error	0.74 Å
I(0) (实空间) i0_real	9.2410e+07
I(0) 误差 (实空间) i0_real_error	1.4630e+06
Rg (倒空间) rg_reciprocal	33.98 Å
I(0) (倒空间) i0_reciprocal	92410000.0000
解质量估计 total_estimate	0.8694
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	31.8 Å
偏度 Skewness skewness	0.319
峰度 Kurtosis kurtosis	-0.761
角度范围 angular_range	— – 0.2350 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	10670000.0000
实空间数据点数 n_real_points	48
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.887; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.875; Smooth: 0.762

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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 (2)

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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	d1gs0a1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.41 — Domain of poly(ADP-ribose) polymerase
超家族 Superfamily superfamily	a.41.1 — Domain of poly(ADP-ribose) polymerase
家族 Family family	a.41.1.1 — Domain of poly(ADP-ribose) polymerase

结构域编号 domain_id	d1gs0a2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.166 — ADP-ribosylation
超家族 Superfamily superfamily	d.166.1 — ADP-ribosylation
家族 Family family	d.166.1.2 — Poly(ADP-ribose) polymerase, C-terminal domain

结构域编号 domain_id	d1gs0b1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.41 — Domain of poly(ADP-ribose) polymerase
超家族 Superfamily superfamily	a.41.1 — Domain of poly(ADP-ribose) polymerase
家族 Family family	a.41.1.1 — Domain of poly(ADP-ribose) polymerase

结构域编号 domain_id	d1gs0b2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.166 — ADP-ribosylation
超家族 Superfamily superfamily	d.166.1 — ADP-ribosylation
家族 Family family	d.166.1.2 — Poly(ADP-ribose) polymerase, C-terminal domain

CATH v4.4 (4 domains)

结构域编号 domain_id	1gs0A01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	142 — Poly(ADP-ribose) Polymerase; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Poly(ADP-ribose) polymerase, regulatory domain

结构域编号 domain_id	1gs0A02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	228 — Phosphoenolpyruvate Carboxykinase; domain 3
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1gs0B01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	142 — Poly(ADP-ribose) Polymerase; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Poly(ADP-ribose) polymerase, regulatory domain

结构域编号 domain_id	1gs0B02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	228 — Phosphoenolpyruvate Carboxykinase; domain 3
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	83.650 Å
晶胞边长 b length_b	85.820 Å
晶胞边长 c length_c	139.460 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	8

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	2.800 Å
最低分辨率 resolution_low	29.950 Å
R 因子 r_factor	0.2440
R_work r_work	0.2440
R_free r_free	0.2680

描述 description	POLY (ADP-RIBOSE) POLYMERASE-2
分子量 formula_weight	39697.7 kDa
EC 编号 ec_number	2.4.2.30
来源方法 src_method	man
拷贝数 entity_count	2

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	5536

Crystal structure of the catalytic fragment of murine poly(ADP-ribose) polymerase-2

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 (2)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 water

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	MUS MUSCULUS
通用名 common_name	MOUSE
NCBI 分类编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	SPODOPTERA FRUGIPERDA

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	75

fit	/app/data/saxs_computation/gs/1gs0/1gs0.fit
pddf	/app/data/pr_computation/gs/1gs0/1gs0.pr.out
profile	/app/data/saxs_computation/gs/1gs0/1gs0.dat