SAXSdb — 1yf0

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1yf0
沉积日期 deposition_date	2004-12-29
结构标题 title	Structural and biochemical analysis of the link between enzymatic activity and oligomerization in AhpC, a bacterial peroxiredoxin.
关键词 keywords	peroxiredoxin, AhpC, Alkyl hydroperoxide reductase subunit C, OXIDOREDUCTASE; OXIDOREDUCTASE
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	37.34 Å
回转半径 Rg (电子) rg_electron	37.31 Å
零角强度 I(0) i0	135284000.00
分子量 molecular_weight	93007.0 kDa
排除体积 excluded_volume	115770 Å³
包络体积 envelope_volume	152380 Å³
水化壳体积 shell_volume	35586 Å³
包络直径 envelope_diameter	126.7 Å
壳层 Rg shell_rg	41.37 Å
包络 Rg envelope_rg	36.74 Å
形状 Rg shape_rg	37.30 Å
总 Rg total_rg	37.63 Å
总原子数 total_atoms	6556
残基数 n_residues	826
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	125.9 Å
Rg (实空间) rg_real	37.65 Å
Rg 误差 (实空间) rg_real_error	1.20 Å
I(0) (实空间) i0_real	1.3530e+08
I(0) 误差 (实空间) i0_real_error	2.2470e+06
Rg (倒空间) rg_reciprocal	37.46 Å
I(0) (倒空间) i0_reciprocal	135300000.0000
解质量估计 total_estimate	0.8223
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	27.0 Å
偏度 Skewness skewness	0.394
峰度 Kurtosis kurtosis	-0.720
角度范围 angular_range	— – 0.2100 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	37480000.0000
实空间数据点数 n_real_points	43
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.713; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.705; Smooth: 0.841

▶

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

▶

5. 实体与聚合体信息 (3)

Entity 1 polymer

描述 description	Alkyl hydroperoxide reductase subunit C
分子量 formula_weight	20653.2 kDa
EC 编号 ec_number	1.11.1.15
突变 mutation	T77I
来源方法 src_method	man
拷贝数 entity_count	5

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E
原子数 atom_count	6987

SLINTKIKPFKNQAFKNGEFIEVTEKDTEGRWSVFFFYPADFTFVCPTELGDVADHYEELQKLGVDVYSVSTDTHFIHKAWHSSSETIAKIKYAMIGDPTGALTRNFDNMREDEGLADRATFVVDPQGIIQAIEVTAEGIGRDASDLLRKIKAAQYVAAHPGEVCPAKWKEGEATLAPSLDLVGKI

来源 Source

来源生物 organism	Salmonella typhimurium
NCBI 分类编号 ncbi_taxonomy_id	602
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	10

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	431

▼

6. 折叠分类 (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

结构域编号 domain_id	d1yf0a1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.47 — Thioredoxin fold
超家族 Superfamily superfamily	c.47.1 — Thioredoxin-like
家族 Family family	c.47.1.10 — Glutathione peroxidase-like

结构域编号 domain_id	d1yf0b_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.47 — Thioredoxin fold
超家族 Superfamily superfamily	c.47.1 — Thioredoxin-like
家族 Family family	c.47.1.10 — Glutathione peroxidase-like

结构域编号 domain_id	d1yf0c_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.47 — Thioredoxin fold
超家族 Superfamily superfamily	c.47.1 — Thioredoxin-like
家族 Family family	c.47.1.10 — Glutathione peroxidase-like

结构域编号 domain_id	d1yf0d_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.47 — Thioredoxin fold
超家族 Superfamily superfamily	c.47.1 — Thioredoxin-like
家族 Family family	c.47.1.10 — Glutathione peroxidase-like

结构域编号 domain_id	d1yf0e_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.47 — Thioredoxin fold
超家族 Superfamily superfamily	c.47.1 — Thioredoxin-like
家族 Family family	c.47.1.10 — Glutathione peroxidase-like

CATH v4.4 (5 domains)

结构域编号 domain_id	1yf0A00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	30 — Glutaredoxin
同源超家族 H-superfamily homologous superfamily	10 — Glutaredoxin

结构域编号 domain_id	1yf0B00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	30 — Glutaredoxin
同源超家族 H-superfamily homologous superfamily	10 — Glutaredoxin

结构域编号 domain_id	1yf0C00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	30 — Glutaredoxin
同源超家族 H-superfamily homologous superfamily	10 — Glutaredoxin

结构域编号 domain_id	1yf0D00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	30 — Glutaredoxin
同源超家族 H-superfamily homologous superfamily	10 — Glutaredoxin

结构域编号 domain_id	1yf0E00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	30 — Glutaredoxin
同源超家族 H-superfamily homologous superfamily	10 — Glutaredoxin

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	127.450 Å
晶胞边长 b length_b	170.870 Å
晶胞边长 c length_c	135.900 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	40

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	2.500 Å
最低分辨率 resolution_low	100.000 Å
R 因子 r_factor	0.1743
R_work r_work	0.1743
R_free r_free	0.2284

fit	/app/data/saxs_computation/yf/1yf0/1yf0.fit
pddf	/app/data/pr_computation/yf/1yf0/1yf0.pr.out
profile	/app/data/saxs_computation/yf/1yf0/1yf0.dat

Structural and biochemical analysis of the link between enzymatic activity and oligomerization in AhpC, a bacterial peroxiredoxin.

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

来源 Source

Entity 2 non-polymer

Entity 3 water

6. 折叠分类 (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

CATH v4.4 (5 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)