SAXSdb — 2gyk

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2gyk
沉积日期 deposition_date	2006-05-09
结构标题 title	Crystal structure of the complex of the Colicin E9 DNase domain with a mutant immunity protein, IMME9 (D51A)
关键词 keywords	PROTEIN-PROTEIN COMPLEX, 4-HELIX BUNDLE, DNASE DOMAIN, HNH-MOTIF, antibiotic-antibiotic inhibitor COMPLEX; antibiotic/antibiotic inhibitor
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	47.19 Å
回转半径 Rg (电子) rg_electron	48.18 Å
零角强度 I(0) i0	37043600.00
分子量 molecular_weight	48135.0 kDa
排除体积 excluded_volume	59409 Å³
包络体积 envelope_volume	91986 Å³
水化壳体积 shell_volume	16380 Å³
包络直径 envelope_diameter	156.1 Å
壳层 Rg shell_rg	51.11 Å
包络 Rg envelope_rg	45.82 Å
形状 Rg shape_rg	48.20 Å
总 Rg total_rg	48.26 Å
总原子数 total_atoms	3385
残基数 n_residues	428
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	154.8 Å
Rg (实空间) rg_real	48.20 Å
Rg 误差 (实空间) rg_real_error	2.50 Å
I(0) (实空间) i0_real	3.7040e+07
I(0) 误差 (实空间) i0_real_error	7.9560e+05
Rg (倒空间) rg_reciprocal	47.20 Å
I(0) (倒空间) i0_reciprocal	37000000.0000
解质量估计 total_estimate	0.5525
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	23.4 Å
偏度 Skewness skewness	0.309
峰度 Kurtosis kurtosis	-1.215
角度范围 angular_range	— – 0.1650 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	920700.0000
实空间数据点数 n_real_points	34
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.001; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.003; Smooth: 0.178

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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	Colicin-E9 immunity protein
分子量 formula_weight	9548.5 kDa
突变 mutation	D51A
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,E
原子数 atom_count	4109

MELKHSISDYTEAEFLQLVTTICNADTSSEEELVKLVTHFEEMTEHPSGSALIYYPKEGDDDSPSGIVNTVKQWRAANGKSGFKQG

来源 Source

来源生物 organism	Escherichia coli K12
NCBI 分类编号 ncbi_taxonomy_id	83333
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

描述 description	Colicin-E9
分子量 formula_weight	15120.0 kDa
EC 编号 ec_number	3.1.21.1
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,F

MESKRNKPGKATGKGKPVGDKWLDDAGKDSGAPIPDRIADKLRDKEFKSFDDFRKAVWEEVSKDPELSKNLNPSNKSSVSKGYSPFTPKNQQVGGRKVYELHHDKPISQGGEVYDMDNIRVTTPKRHIDIHRGK

来源 Source

来源生物 organism	Escherichia coli K12
NCBI 分类编号 ncbi_taxonomy_id	83333
宿主生物 host_organism	Escherichia coli

Entity 3 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 non-polymer

描述 description	PHOSPHATE ION
分子量 formula_weight	95.0 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	686

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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	d2gyka1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.28 — Acyl carrier protein-like
超家族 Superfamily superfamily	a.28.2 — Colicin E immunity proteins
家族 Family family	a.28.2.1 — Colicin E immunity proteins

结构域编号 domain_id	d2gykb_
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	d2gyke_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.28 — Acyl carrier protein-like
超家族 Superfamily superfamily	a.28.2 — Colicin E immunity proteins
家族 Family family	a.28.2.1 — Colicin E immunity proteins

结构域编号 domain_id	d2gykf_
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	2gykA00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1200 — Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A
同源超家族 H-superfamily homologous superfamily	20 — Colicin E immunity protein

结构域编号 domain_id	2gykB00
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	2gykE00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1200 — Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A
同源超家族 H-superfamily homologous superfamily	20 — Colicin E immunity protein

结构域编号 domain_id	2gykF00
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	44.903 Å
晶胞边长 b length_b	88.248 Å
晶胞边长 c length_c	52.235 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	91.92 °
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	1.600 Å
最低分辨率 resolution_low	19.860 Å
R 因子 r_factor	0.1870
R_work r_work	0.1850
R_free r_free	0.2320

fit	/app/data/saxs_computation/gy/2gyk/2gyk.fit
pddf	/app/data/pr_computation/gy/2gyk/2gyk.pr.out
profile	/app/data/saxs_computation/gy/2gyk/2gyk.dat

Crystal structure of the complex of the Colicin E9 DNase domain with a mutant immunity protein, IMME9 (D51A)

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) 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)