SAXSdb — 1v14

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1v14
沉积日期 deposition_date	2004-04-06
结构标题 title	Crystal Structure of the Colicin E9, mutant His103Ala, in complex with Mg+2 and dsDNA (resolution 2.9A)
关键词 keywords	HOMING ENDONUCLEASES, COLICIN, HNH MOTIF, BETA-BETA-ALPHA METAL MOTIF, HYDROLASE; HYDROLASE
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	30.93 Å
回转半径 Rg (电子) rg_electron	30.57 Å
零角强度 I(0) i0	126904000.00
分子量 molecular_weight	76119.0 kDa
排除体积 excluded_volume	89668 Å³
包络体积 envelope_volume	124570 Å³
水化壳体积 shell_volume	34481 Å³
包络直径 envelope_diameter	99.6 Å
壳层 Rg shell_rg	37.29 Å
包络 Rg envelope_rg	30.18 Å
形状 Rg shape_rg	30.55 Å
总 Rg total_rg	31.15 Å
总原子数 total_atoms	5295
残基数 n_residues	582
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	97.4 Å
Rg (实空间) rg_real	30.87 Å
Rg 误差 (实空间) rg_real_error	0.81 Å
I(0) (实空间) i0_real	1.2690e+08
I(0) 误差 (实空间) i0_real_error	1.8980e+06
Rg (倒空间) rg_reciprocal	30.90 Å
I(0) (倒空间) i0_reciprocal	126900000.0000
解质量估计 total_estimate	0.9063
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	42.0 Å
偏度 Skewness skewness	0.185
峰度 Kurtosis kurtosis	-0.632
角度范围 angular_range	— – 0.2550 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	31540000.0000
实空间数据点数 n_real_points	52
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.954; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.937

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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 (4)

Entity 1 polymer

描述 description	COLICIN E9
分子量 formula_weight	15053.0 kDa
EC 编号 ec_number	3.1.21.1
突变 mutation	YES
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
原子数 atom_count	5328

MESKRNKPGKATGKGKPVGDKWLDDAGKDSGAPIPDRIADKLRDKEFKSFDDFRKAVWEEVSKDPELSKNLNPSNKSSVSKGYSPFTPKNQQVGGRKVYELHADKPISQGGEVYDMDNIRVTTPKRHIDIHRGK

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 2 polymer

描述 description	5'-D(GPCPGPAPTPCPGPCP)-3'
分子量 formula_weight	2427.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	8

聚合体 Polymer

聚合体类型 type	polydeoxyribonucleotide
链编号 strand_id	E,F,G,H,I,J,K,L

GCGATCGC

Entity 3 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

Entity 4 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	33

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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	d1v14a_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.4 — His-Me finger endonucleases
超家族 Superfamily superfamily	d.4.1 — His-Me finger endonucleases
家族 Family family	d.4.1.1 — HNH-motif

结构域编号 domain_id	d1v14b_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.4 — His-Me finger endonucleases
超家族 Superfamily superfamily	d.4.1 — His-Me finger endonucleases
家族 Family family	d.4.1.1 — HNH-motif

结构域编号 domain_id	d1v14c_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.4 — His-Me finger endonucleases
超家族 Superfamily superfamily	d.4.1 — His-Me finger endonucleases
家族 Family family	d.4.1.1 — HNH-motif

结构域编号 domain_id	d1v14d_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.4 — His-Me finger endonucleases
超家族 Superfamily superfamily	d.4.1 — His-Me finger endonucleases
家族 Family family	d.4.1.1 — HNH-motif

CATH v4.4 (4 domains)

结构域编号 domain_id	1v14A00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	540 — Colicin E7 immunity protein; Chain B, fragment: Endonuclease domain
同源超家族 H-superfamily homologous superfamily	10 — Colicin/pyocin, DNase domain

结构域编号 domain_id	1v14B00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	540 — Colicin E7 immunity protein; Chain B, fragment: Endonuclease domain
同源超家族 H-superfamily homologous superfamily	10 — Colicin/pyocin, DNase domain

结构域编号 domain_id	1v14C00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	540 — Colicin E7 immunity protein; Chain B, fragment: Endonuclease domain
同源超家族 H-superfamily homologous superfamily	10 — Colicin/pyocin, DNase domain

结构域编号 domain_id	1v14D00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	540 — Colicin E7 immunity protein; Chain B, fragment: Endonuclease domain
同源超家族 H-superfamily homologous superfamily	10 — Colicin/pyocin, DNase domain

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7. 引用文献 (2)

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晶胞边长 a length_a	92.946 Å
晶胞边长 b length_b	124.442 Å
晶胞边长 c length_c	111.227 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	64

空间群 space_group	C 2 2 21
空间群编号 int_tables_number	20
晶系 crystal_system	—

分辨率 resolution	2.900 Å
最低分辨率 resolution_low	74.540 Å
R 因子 r_factor	0.2190
R_work r_work	0.2150
R_free r_free	0.3060

fit	/app/data/saxs_computation/v1/1v14/1v14.fit
pddf	/app/data/pr_computation/v1/1v14/1v14.pr.out
profile	/app/data/saxs_computation/v1/1v14/1v14.dat

Crystal Structure of the Colicin E9, mutant His103Ala, in complex with Mg+2 and dsDNA (resolution 2.9A)

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 (4)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

Entity 3 non-polymer

Entity 4 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 (2)

8. 文件与曲线 (10)

Files (7)

Curves (3)