2b5u

Crystal Structure Of Colicin E3 V206C Mutant In Complex With Its Immunity Protein

Method: X-RAY DIFFRACTION D_max: 182.0 Å Quality: REASONABLE

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	2b5u
沉积日期 deposition_date	2005-09-29
结构标题 title	Crystal Structure Of Colicin E3 V206C Mutant In Complex With Its Immunity Protein
关键词 keywords	High resolution crystal structure, Colicin E3, Immunity Protein, Ribosome inactivation, RIBOSOME INHIBITOR, HYDROLASE; RIBOSOME INHIBITOR, 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	60.20 Å
回转半径 Rg (电子) rg_electron	61.92 Å
零角强度 I(0) i0	231286000.00
分子量 molecular_weight	121620.0 kDa
排除体积 excluded_volume	150220 Å³
包络体积 envelope_volume	250390 Å³
水化壳体积 shell_volume	37568 Å³
包络直径 envelope_diameter	191.4 Å
壳层 Rg shell_rg	51.62 Å
包络 Rg envelope_rg	59.76 Å
形状 Rg shape_rg	61.99 Å
总 Rg total_rg	61.36 Å
总原子数 total_atoms	8572
残基数 n_residues	1108
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	182.0 Å
Rg (实空间) rg_real	61.25 Å
Rg 误差 (实空间) rg_real_error	2.30 Å
I(0) (实空间) i0_real	2.3130e+08
I(0) 误差 (实空间) i0_real_error	4.7270e+06
Rg (倒空间) rg_reciprocal	59.21 Å
I(0) (倒空间) i0_reciprocal	230500000.0000
解质量估计 total_estimate	0.6326
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	35.0 Å
偏度 Skewness skewness	0.379
峰度 Kurtosis kurtosis	-1.098
角度范围 angular_range	— – 0.1300 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	6076000.0000
实空间数据点数 n_real_points	27
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.342; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.193; 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 (4)

Entity 1 polymer

描述 description	Colicin E3
分子量 formula_weight	58047.0 kDa
EC 编号 ec_number	3.1.-.-
突变 mutation	V206C
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,C
原子数 atom_count	8791

MSGGDGRGHNTGAHSTSGNINGGPTGLGVGGGASDGSGWSSENNPWGGGSGSGIHWGGGSGHGNGGGNGNSGGGSGTGGNLSAVAAPVAFGFPALSTPGAGGLAVSISAGALSAAIADIMAALKGPFKFGLWGVALYGVLPSQIAKDDPNMMSKIVTSLPADDITESPVSSLPLDKATVNVNVRVVDDVKDERQNISVVSGVPMSCPVVDAKPTERPGVFTASIPGAPVLNISVNNSTPAVQTLSPGVTNNTDKDVRPAGFTQGGNTRDAVIRFPKDSGHNAVYVSVSDVLSPDQVKQRQDEENRRQQEWDATHPVEAAERNYERARAELNQANEDVARNQERQAKAVQVYNSRKSELDAANKTLADAIAEIKQFNRFAHDPMAGGHRMWQMAGLKAQRAQTDVNNKQAAFDAAAKEKSDADAALSSAMESRKKKEDKKRSAENNLNDEKNKPRKGFKDYGHDYHPAPKTENIKGLGDLKPGIPKTPKQNGGGKRKRWTGDKGRKIYEWDSQHGELEGYRASDGQHLGSFDPKTGNQLKGPDPKRNIKKYL

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 str. K12 substr. W3110

Entity 2 polymer

描述 description	Colicin E3 immunity protein
分子量 formula_weight	9779.6 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

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

GLKLDLTWFDKSTEDFKGEEYSKDFGDDGSVMESLGVPFKDNVNNGCFDVIAEWVPLLQPYFNHQIDISDNEYFVSFDYRDGDW

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 str. K12 substr. W3110

Entity 3 non-polymer

描述 description	CITRIC ACID
分子量 formula_weight	192.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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	219

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6. 折叠分类 (SCOP + CATH) 14 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d2b5ua1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.101 — Ribonuclease domain of colicin E3
超家族 Superfamily superfamily	b.101.1 — Ribonuclease domain of colicin E3
家族 Family family	b.101.1.1 — Ribonuclease domain of colicin E3

结构域编号 domain_id	d2b5ua2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.110 — Cloacin translocation domain
超家族 Superfamily superfamily	b.110.1 — Cloacin translocation domain
家族 Family family	b.110.1.1 — Cloacin translocation domain

结构域编号 domain_id	d2b5ua3
类 Class class	h — Coiled coil proteins
折叠类型 Fold fold	h.4 — Antiparallel coiled-coil
超家族 Superfamily superfamily	h.4.9 — Colicin E3 receptor domain
家族 Family family	h.4.9.1 — Colicin E3 receptor domain

结构域编号 domain_id	d2b5ub_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.26 — FKBP-like
超家族 Superfamily superfamily	d.26.2 — Colicin E3 immunity protein
家族 Family family	d.26.2.1 — Colicin E3 immunity protein

结构域编号 domain_id	d2b5uc1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.101 — Ribonuclease domain of colicin E3
超家族 Superfamily superfamily	b.101.1 — Ribonuclease domain of colicin E3
家族 Family family	b.101.1.1 — Ribonuclease domain of colicin E3

结构域编号 domain_id	d2b5uc2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.110 — Cloacin translocation domain
超家族 Superfamily superfamily	b.110.1 — Cloacin translocation domain
家族 Family family	b.110.1.1 — Cloacin translocation domain

结构域编号 domain_id	d2b5uc3
类 Class class	h — Coiled coil proteins
折叠类型 Fold fold	h.4 — Antiparallel coiled-coil
超家族 Superfamily superfamily	h.4.9 — Colicin E3 receptor domain
家族 Family family	h.4.9.1 — Colicin E3 receptor domain

结构域编号 domain_id	d2b5ud_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.26 — FKBP-like
超家族 Superfamily superfamily	d.26.2 — Colicin E3 immunity protein
家族 Family family	d.26.2.1 — Colicin E3 immunity protein

CATH v4.4 (6 domains)

结构域编号 domain_id	2b5uA02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily	620 — Helix Hairpins

结构域编号 domain_id	2b5uA03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	380 — Ribonuclease domain of colicin e3 (Residues 456-551)
同源超家族 H-superfamily homologous superfamily	10 — Colicin E3-like ribonuclease domain

结构域编号 domain_id	2b5uB00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	50 — Chitinase A; domain 3
同源超家族 H-superfamily homologous superfamily	20 — Cloacin immunity protein

结构域编号 domain_id	2b5uC02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily	620 — Helix Hairpins

结构域编号 domain_id	2b5uC03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	380 — Ribonuclease domain of colicin e3 (Residues 456-551)
同源超家族 H-superfamily homologous superfamily	10 — Colicin E3-like ribonuclease domain

结构域编号 domain_id	2b5uD00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	50 — Chitinase A; domain 3
同源超家族 H-superfamily homologous superfamily	20 — Cloacin immunity protein

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7. 引用文献 (1)

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晶胞边长 a length_a	66.730 Å
晶胞边长 b length_b	192.916 Å
晶胞边长 c length_c	85.385 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	112.98 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

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	2.300 Å
最低分辨率 resolution_low	44.400 Å
R 因子 r_factor	0.2910
R_work r_work	0.2590
R_free r_free	0.2950

fit	/app/data/saxs_computation/b5/2b5u/2b5u.fit
pddf	/app/data/pr_computation/b5/2b5u/2b5u.pr.out
profile	/app/data/saxs_computation/b5/2b5u/2b5u.dat

Crystal Structure Of Colicin E3 V206C Mutant In Complex With Its Immunity Protein

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

来源 Source

Entity 3 non-polymer

Entity 4 water

6. 折叠分类 (SCOP + CATH) 14 domains

SCOP 2.08 (8 domains)

CATH v4.4 (6 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)