SAXSdb — 2h8c

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2h8c
沉积日期 deposition_date	2006-06-07
结构标题 title	Structure of RusA D70N in complex with DNA
关键词 keywords	PROTEIN-DNA COMPLEX, RECOMBINATION, HYDROLASE-DNA COMPLEX; HYDROLASE/DNA
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	31.38 Å
回转半径 Rg (电子) rg_electron	31.97 Å
零角强度 I(0) i0	82074200.00
分子量 molecular_weight	62481.0 kDa
排除体积 excluded_volume	74209 Å³
包络体积 envelope_volume	105730 Å³
水化壳体积 shell_volume	28832 Å³
包络直径 envelope_diameter	110.6 Å
壳层 Rg shell_rg	37.16 Å
包络 Rg envelope_rg	30.96 Å
形状 Rg shape_rg	31.96 Å
总 Rg total_rg	32.42 Å
总原子数 total_atoms	4342
残基数 n_residues	499
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	104.2 Å
Rg (实空间) rg_real	31.48 Å
Rg 误差 (实空间) rg_real_error	1.37 Å
I(0) (实空间) i0_real	8.2070e+07
I(0) 误差 (实空间) i0_real_error	1.4260e+06
Rg (倒空间) rg_reciprocal	31.44 Å
I(0) (倒空间) i0_reciprocal	82070000.0000
解质量估计 total_estimate	0.8959
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	33.4 Å
偏度 Skewness skewness	0.368
峰度 Kurtosis kurtosis	-0.403
角度范围 angular_range	— – 0.2500 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	4649000.0000
实空间数据点数 n_real_points	51
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.912; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.971; Smooth: 0.938

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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 (3)

Entity 1 polymer

描述 description	5'-D(CPCPGPGPTPAPCPCPGPGP*T)-3'
分子量 formula_weight	3350.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polydeoxyribonucleotide
链编号 strand_id	Y,Z,W,X
原子数 atom_count	4357

CCGGTACCGGT

Entity 2 polymer

描述 description	Crossover junction endodeoxyribonuclease rusA
分子量 formula_weight	13866.9 kDa
EC 编号 ec_number	3.1.22.-
突变 mutation	D70N
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

MNTYSITLPWPPSNNRYYRHNRGRTHVSAEGQAYRDNVARIIKNAMLDIGLAMPVKIRIECHMPDRRRRNLDNLQKAAFDALTKAGFWLDDAQVVDYRVVKMPVTKGGRLELTITEMGNE

来源 Source

来源生物 organism	Escherichia coli
NCBI 分类编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 3 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	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	d2h8ca_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.79 — Bacillus chorismate mutase-like
超家族 Superfamily superfamily	d.79.6 — Holliday junction resolvase RusA
家族 Family family	d.79.6.1 — Holliday junction resolvase RusA

结构域编号 domain_id	d2h8cb_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.79 — Bacillus chorismate mutase-like
超家族 Superfamily superfamily	d.79.6 — Holliday junction resolvase RusA
家族 Family family	d.79.6.1 — Holliday junction resolvase RusA

结构域编号 domain_id	d2h8cc_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.79 — Bacillus chorismate mutase-like
超家族 Superfamily superfamily	d.79.6 — Holliday junction resolvase RusA
家族 Family family	d.79.6.1 — Holliday junction resolvase RusA

结构域编号 domain_id	d2h8cd_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.79 — Bacillus chorismate mutase-like
超家族 Superfamily superfamily	d.79.6 — Holliday junction resolvase RusA
家族 Family family	d.79.6.1 — Holliday junction resolvase RusA

CATH v4.4 (4 domains)

结构域编号 domain_id	2h8cA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
同源超家族 H-superfamily homologous superfamily	70 — Holliday junction resolvase RusA

结构域编号 domain_id	2h8cB00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
同源超家族 H-superfamily homologous superfamily	70 — Holliday junction resolvase RusA

结构域编号 domain_id	2h8cC00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
同源超家族 H-superfamily homologous superfamily	70 — Holliday junction resolvase RusA

结构域编号 domain_id	2h8cD00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
同源超家族 H-superfamily homologous superfamily	70 — Holliday junction resolvase RusA

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7. 引用文献 (1)

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晶胞边长 a length_a	64.616 Å
晶胞边长 b length_b	59.483 Å
晶胞边长 c length_c	90.721 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	101.59 °
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	3.100 Å
最低分辨率 resolution_low	44.460 Å
R 因子 r_factor	0.2490
R_work r_work	0.2470
R_free r_free	0.2890

fit	/app/data/saxs_computation/h8/2h8c/2h8c.fit
pddf	/app/data/pr_computation/h8/2h8c/2h8c.pr.out
profile	/app/data/saxs_computation/h8/2h8c/2h8c.dat

Structure of RusA D70N in complex with DNA

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 (3)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 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)