1ped

BACTERIAL SECONDARY ALCOHOL DEHYDROGENASE (APO-FORM)

Method: X-RAY DIFFRACTION D_max: 94.4 Å Quality: GOOD

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

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1ped
沉积日期 deposition_date	1995-12-28
结构标题 title	BACTERIAL SECONDARY ALCOHOL DEHYDROGENASE (APO-FORM)
关键词 keywords	THERMOSTABLE, OXIDOREDUCTASE, ZINC, NADP; 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	32.57 Å
回转半径 Rg (电子) rg_electron	32.03 Å
零角强度 I(0) i0	347020000.00
分子量 molecular_weight	151120.0 kDa
排除体积 excluded_volume	189690 Å³
包络体积 envelope_volume	222360 Å³
水化壳体积 shell_volume	55261 Å³
包络直径 envelope_diameter	98.0 Å
壳层 Rg shell_rg	40.95 Å
包络 Rg envelope_rg	31.95 Å
形状 Rg shape_rg	32.07 Å
总 Rg total_rg	32.52 Å
总原子数 total_atoms	10564
残基数 n_residues	1404
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	94.4 Å
Rg (实空间) rg_real	32.31 Å
Rg 误差 (实空间) rg_real_error	0.47 Å
I(0) (实空间) i0_real	3.4700e+08
I(0) 误差 (实空间) i0_real_error	4.8550e+06
Rg (倒空间) rg_reciprocal	32.42 Å
I(0) (倒空间) i0_reciprocal	347100000.0000
解质量估计 total_estimate	0.8952
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	42.4 Å
偏度 Skewness skewness	0.082
峰度 Kurtosis kurtosis	-0.563
角度范围 angular_range	— – 0.2450 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	164900000.0000
实空间数据点数 n_real_points	50
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.973; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.978; Smooth: 0.737

▶

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	NADP-DEPENDENT ALCOHOL DEHYDROGENASE
分子量 formula_weight	37762.9 kDa
EC 编号 ec_number	1.1.1.2
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	11122

MKGFAMLGINKLGWIEKERPVAGSYDAIVRPLAVSPCTSDIHTVFEGALGDRKNMILGHEAVGEVVEVGSEVKDFKPGDRVIVPCTTPDWRSLEVQAGFQQHSNGMLAGWKFSNFKDGVFGEYFHVNDADMNLAILPKDMPLENAVMITDMMTTGFHGAELADIQMGSSVVVIGIGAVGLMGIAGAKLRGAGRIIGVGSRPICVEAAKFYGATDILNYKNGHIVDQVMKLTNGKGVDRVIMAGGGSETLSQAVSMVKPGGIISNINYHGSGDALLIPRVEWGCGMAHKTIKGGLCPGGRLRAEMLRDMVVYNRVDLSKLVTHVYHGFDHIEEALLLMKDKPKDLIKAVVIL

来源 Source

来源生物 organism	Clostridium beijerinckii
NCBI 分类编号 ncbi_taxonomy_id	1520
宿主生物 host_organism	Escherichia coli

Entity 2 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	4

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	558

▼

6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d1peda1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.35 — GroES-like
超家族 Superfamily superfamily	b.35.1 — GroES-like
家族 Family family	b.35.1.2 — Alcohol dehydrogenase-like, N-terminal domain

结构域编号 domain_id	d1peda2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family family	c.2.1.1 — Alcohol dehydrogenase-like, C-terminal domain

结构域编号 domain_id	d1pedb1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.35 — GroES-like
超家族 Superfamily superfamily	b.35.1 — GroES-like
家族 Family family	b.35.1.2 — Alcohol dehydrogenase-like, N-terminal domain

结构域编号 domain_id	d1pedb2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family family	c.2.1.1 — Alcohol dehydrogenase-like, C-terminal domain

结构域编号 domain_id	d1pedc1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.35 — GroES-like
超家族 Superfamily superfamily	b.35.1 — GroES-like
家族 Family family	b.35.1.2 — Alcohol dehydrogenase-like, N-terminal domain

结构域编号 domain_id	d1pedc2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family family	c.2.1.1 — Alcohol dehydrogenase-like, C-terminal domain

结构域编号 domain_id	d1pedd1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.35 — GroES-like
超家族 Superfamily superfamily	b.35.1 — GroES-like
家族 Family family	b.35.1.2 — Alcohol dehydrogenase-like, N-terminal domain

结构域编号 domain_id	d1pedd2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family family	c.2.1.1 — Alcohol dehydrogenase-like, C-terminal domain

CATH v4.4 (8 domains)

结构域编号 domain_id	1pedA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	180 — Quinone Oxidoreductase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Medium-chain alcohol dehydrogenases, catalytic domain

结构域编号 domain_id	1pedA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

结构域编号 domain_id	1pedB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	180 — Quinone Oxidoreductase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Medium-chain alcohol dehydrogenases, catalytic domain

结构域编号 domain_id	1pedB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

结构域编号 domain_id	1pedC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	180 — Quinone Oxidoreductase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Medium-chain alcohol dehydrogenases, catalytic domain

结构域编号 domain_id	1pedC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

结构域编号 domain_id	1pedD01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	180 — Quinone Oxidoreductase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Medium-chain alcohol dehydrogenases, catalytic domain

结构域编号 domain_id	1pedD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	80.400 Å
晶胞边长 b length_b	102.260 Å
晶胞边长 c length_c	193.500 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	16

空间群 space_group	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	2.150 Å
最低分辨率 resolution_low	50.000 Å
R 因子 r_factor	0.2150
R_work r_work	0.2150
R_free r_free	0.2580

fit	/app/data/saxs_computation/pe/1ped/1ped.fit
pddf	/app/data/pr_computation/pe/1ped/1ped.pr.out
profile	/app/data/saxs_computation/pe/1ped/1ped.dat