SAXSdb — 2bnz

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2bnz
沉积日期 deposition_date	2005-04-06
结构标题 title	Structural basis for cooperative binding of Ribbon-Helix-Helix Omega repressor to inverted DNA heptad repeats
关键词 keywords	DNA BINDING PROTEIN-DNA COMPLEX, RIBBON-HELIX-HELIX, RHH, METJ/ARC SUPERFAMILY, COOPERATIVE DNA BINDING, INC18 FAMILY; DNA BINDING PROTEIN/DNA
实验方法 method	X-RAY DIFFRACTION

▼

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	23.86 Å
回转半径 Rg (电子) rg_electron	23.49 Å
零角强度 I(0) i0	35544800.00
分子量 molecular_weight	37028.0 kDa
排除体积 excluded_volume	42541 Å³
包络体积 envelope_volume	56439 Å³
水化壳体积 shell_volume	21050 Å³
包络直径 envelope_diameter	117.2 Å
壳层 Rg shell_rg	28.57 Å
包络 Rg envelope_rg	26.14 Å
形状 Rg shape_rg	23.46 Å
总 Rg total_rg	24.07 Å
总原子数 total_atoms	2540
残基数 n_residues	244
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

▼

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	62.6 Å
Rg (实空间) rg_real	22.22 Å
Rg 误差 (实空间) rg_real_error	0.10 Å
I(0) (实空间) i0_real	3.3690e+07
I(0) 误差 (实空间) i0_real_error	3.3210e+05
Rg (倒空间) rg_reciprocal	24.25 Å
I(0) (倒空间) i0_reciprocal	35540000.0000
解质量估计 total_estimate	0.6853
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	25.4 Å
偏度 Skewness skewness	0.330
峰度 Kurtosis kurtosis	-0.505
角度范围 angular_range	— – 0.3350 Å⁻¹
当前正则化参数 α current_alpha	3.3290
最高正则化参数 α highest_alpha	3295000.0000
实空间数据点数 n_real_points	65
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.017; Oscil: 0.994; Stabil: 0.979; Sysdev: 0.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.000

▶

4. 晶体学与实验 4. Crystallography & Experiment

▶

5. 实体与聚合体信息 (4)

Entity 1 polymer

描述 description	ORF OMEGA
分子量 formula_weight	6137.2 kDa
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	2585

MAKKDIMGDKTVRVRADLHHIIKIETAKNGGNVKEVMDQALEEYIRKYLPDKL

来源 Source

来源生物 organism	STREPTOCOCCUS PYOGENES
NCBI 分类编号 ncbi_taxonomy_id	1314
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 polymer

描述 description	;5'-D(GPAPAPTPCPAPCPAPAPGP TPGPAPTPTPAPGPC)-3' ;
分子量 formula_weight	5548.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polydeoxyribonucleotide
链编号 strand_id	E,G

GAATCACAAGTGATTAGC

Entity 3 polymer

描述 description	;5'-D(CPTPAPAPTPCPAPCPTPTP GPTPGPAPTPTPCPG)-3' ;
分子量 formula_weight	5481.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polydeoxyribonucleotide
链编号 strand_id	F,H

CTAATCACTTGTGATTCG

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	45

▼

6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d2bnza_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.43 — Ribbon-helix-helix
超家族 Superfamily superfamily	a.43.1 — Ribbon-helix-helix
家族 Family family	a.43.1.4 — Omega transcriptional repressor

结构域编号 domain_id	d2bnzb_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.43 — Ribbon-helix-helix
超家族 Superfamily superfamily	a.43.1 — Ribbon-helix-helix
家族 Family family	a.43.1.4 — Omega transcriptional repressor

结构域编号 domain_id	d2bnzc_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.43 — Ribbon-helix-helix
超家族 Superfamily superfamily	a.43.1 — Ribbon-helix-helix
家族 Family family	a.43.1.4 — Omega transcriptional repressor

结构域编号 domain_id	d2bnzd_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.43 — Ribbon-helix-helix
超家族 Superfamily superfamily	a.43.1 — Ribbon-helix-helix
家族 Family family	a.43.1.4 — Omega transcriptional repressor

CATH v4.4 (4 domains)

结构域编号 domain_id	2bnzA00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1220 — Arc Repressor Mutant
同源超家族 H-superfamily homologous superfamily	10 — Met repressor-like

结构域编号 domain_id	2bnzB00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1220 — Arc Repressor Mutant
同源超家族 H-superfamily homologous superfamily	10 — Met repressor-like

结构域编号 domain_id	2bnzC00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1220 — Arc Repressor Mutant
同源超家族 H-superfamily homologous superfamily	10 — Met repressor-like

结构域编号 domain_id	2bnzD00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1220 — Arc Repressor Mutant
同源超家族 H-superfamily homologous superfamily	10 — Met repressor-like

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	75.991 Å
晶胞边长 b length_b	42.505 Å
晶胞边长 c length_c	103.727 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	107.17 °
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	2.600 Å
最低分辨率 resolution_low	100.000 Å
R 因子 r_factor	0.2270
R_work r_work	0.2250
R_free r_free	0.2580

fit	/app/data/saxs_computation/bn/2bnz/2bnz.fit
pddf	/app/data/pr_computation/bn/2bnz/2bnz.pr.out
profile	/app/data/saxs_computation/bn/2bnz/2bnz.dat

Structural basis for cooperative binding of Ribbon-Helix-Helix Omega repressor to inverted DNA heptad repeats

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 polymer

聚合体 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 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)