1zum

Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, Apo Form

Method: X-RAY DIFFRACTION D_max: 215.4 Å Quality: EXCELLENT

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	1zum
沉积日期 deposition_date	2005-05-31
结构标题 title	Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, Apo Form
关键词 keywords	Rossmann fold, OXIDOREDUCTASE; OXIDOREDUCTASE
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	77.64 Å
回转半径 Rg (电子) rg_electron	78.78 Å
零角强度 I(0) i0	5169930000.00
分子量 molecular_weight	615320.0 kDa
排除体积 excluded_volume	772600 Å³
包络体积 envelope_volume	1110600 Å³
水化壳体积 shell_volume	129400 Å³
包络直径 envelope_diameter	270.2 Å
壳层 Rg shell_rg	62.69 Å
包络 Rg envelope_rg	77.45 Å
形状 Rg shape_rg	78.77 Å
总 Rg total_rg	78.55 Å
总原子数 total_atoms	43353
残基数 n_residues	5598
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	215.4 Å
Rg (实空间) rg_real	74.30 Å
Rg 误差 (实空间) rg_real_error	1.07 Å
I(0) (实空间) i0_real	5.0210e+09
I(0) 误差 (实空间) i0_real_error	9.5910e+07
Rg (倒空间) rg_reciprocal	74.38 Å
I(0) (倒空间) i0_reciprocal	5126000000.0000
解质量估计 total_estimate	0.9182
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	53.8 Å
偏度 Skewness skewness	0.517
峰度 Kurtosis kurtosis	-0.559
角度范围 angular_range	— – 0.1000 Å⁻¹
当前正则化参数 α current_alpha	0.1866
最高正则化参数 α highest_alpha	353400000.0000
实空间数据点数 n_real_points	21
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.842; Stabil: 0.976; Sysdev: 1.000; Positv: 1.000; Valcen: 0.971; Smooth: 0.648

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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	Aldehyde dehydrogenase
分子量 formula_weight	54499.7 kDa
EC 编号 ec_number	1.2.1.3
突变 mutation	E487K
来源方法 src_method	man
拷贝数 entity_count	12

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F,G,H,I,J,K,L
原子数 atom_count	46002

SAAATQAVPAPNQQPEVFCNQIFINNEWHDAVSRKTFPTVNPSTGEVICQVAEGDKEDVDKAVKAARAAFQLGSPWRRMDASHRGRLLNRLADLIERDRTYLAALETLDNGKPYVISYLVDLDMVLKCLRYYAGWADKYHGKTIPIDGDFFSYTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAEQTPLTALYVANLIKEAGFPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIGRVIQVAAGSSNLKRVTLELGGKSPNIIMSDADMDWAVEQAHFALFFNQGQCCCAGSRTFVQEDIYDEFVERSVARAKSRVVGNPFDSKTEQGPQVDETQFKKILGYINTGKQEGAKLLCGGGIAADRGYFIQPTVFGDVQDGMTIAKEEIFGPVMQILKFKTIEEVVGRANNSTYGLAAAVFTKDLDKANYLSQALQAGTVWVNCYDVFGAQSPFGGYKMSGSGRELGEYGLQAYTKVKTVTVKVPQKNS

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21

Entity 2 non-polymer

描述 description	SODIUM ION
分子量 formula_weight	23.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	12

Entity 3 non-polymer

描述 description	GUANIDINE
分子量 formula_weight	59.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	8

Entity 4 non-polymer

描述 description	1,2-ETHANEDIOL
分子量 formula_weight	62.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	21

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	2649

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6. 折叠分类 (SCOP + CATH) 36 domains

SCOP 2.08 (12 domains)

结构域编号 domain_id	d1zuma_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.82 — ALDH-like
超家族 Superfamily superfamily	c.82.1 — ALDH-like
家族 Family family	c.82.1.1 — ALDH-like

结构域编号 domain_id	d1zumb_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.82 — ALDH-like
超家族 Superfamily superfamily	c.82.1 — ALDH-like
家族 Family family	c.82.1.1 — ALDH-like

结构域编号 domain_id	d1zumc_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.82 — ALDH-like
超家族 Superfamily superfamily	c.82.1 — ALDH-like
家族 Family family	c.82.1.1 — ALDH-like

结构域编号 domain_id	d1zumd_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.82 — ALDH-like
超家族 Superfamily superfamily	c.82.1 — ALDH-like
家族 Family family	c.82.1.1 — ALDH-like

结构域编号 domain_id	d1zume_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.82 — ALDH-like
超家族 Superfamily superfamily	c.82.1 — ALDH-like
家族 Family family	c.82.1.1 — ALDH-like

结构域编号 domain_id	d1zumf_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.82 — ALDH-like
超家族 Superfamily superfamily	c.82.1 — ALDH-like
家族 Family family	c.82.1.1 — ALDH-like

结构域编号 domain_id	d1zumg_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.82 — ALDH-like
超家族 Superfamily superfamily	c.82.1 — ALDH-like
家族 Family family	c.82.1.1 — ALDH-like

结构域编号 domain_id	d1zumh_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.82 — ALDH-like
超家族 Superfamily superfamily	c.82.1 — ALDH-like
家族 Family family	c.82.1.1 — ALDH-like

结构域编号 domain_id	d1zumi_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.82 — ALDH-like
超家族 Superfamily superfamily	c.82.1 — ALDH-like
家族 Family family	c.82.1.1 — ALDH-like

结构域编号 domain_id	d1zumj_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.82 — ALDH-like
超家族 Superfamily superfamily	c.82.1 — ALDH-like
家族 Family family	c.82.1.1 — ALDH-like

结构域编号 domain_id	d1zumk_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.82 — ALDH-like
超家族 Superfamily superfamily	c.82.1 — ALDH-like
家族 Family family	c.82.1.1 — ALDH-like

结构域编号 domain_id	d1zuml_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.82 — ALDH-like
超家族 Superfamily superfamily	c.82.1 — ALDH-like
家族 Family family	c.82.1.1 — ALDH-like

CATH v4.4 (24 domains)

结构域编号 domain_id	1zumA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	605 — Aldehyde Dehydrogenase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aldehyde Dehydrogenase; Chain A, domain 1

结构域编号 domain_id	1zumA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	309 — Aldehyde Dehydrogenase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Aldehyde Dehydrogenase; Chain A, domain 2

结构域编号 domain_id	1zumB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	605 — Aldehyde Dehydrogenase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aldehyde Dehydrogenase; Chain A, domain 1

结构域编号 domain_id	1zumB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	309 — Aldehyde Dehydrogenase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Aldehyde Dehydrogenase; Chain A, domain 2

结构域编号 domain_id	1zumC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	605 — Aldehyde Dehydrogenase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aldehyde Dehydrogenase; Chain A, domain 1

结构域编号 domain_id	1zumC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	309 — Aldehyde Dehydrogenase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Aldehyde Dehydrogenase; Chain A, domain 2

结构域编号 domain_id	1zumD01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	605 — Aldehyde Dehydrogenase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aldehyde Dehydrogenase; Chain A, domain 1

结构域编号 domain_id	1zumD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	309 — Aldehyde Dehydrogenase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Aldehyde Dehydrogenase; Chain A, domain 2

结构域编号 domain_id	1zumE01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	605 — Aldehyde Dehydrogenase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aldehyde Dehydrogenase; Chain A, domain 1

结构域编号 domain_id	1zumE02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	309 — Aldehyde Dehydrogenase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Aldehyde Dehydrogenase; Chain A, domain 2

结构域编号 domain_id	1zumF01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	605 — Aldehyde Dehydrogenase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aldehyde Dehydrogenase; Chain A, domain 1

结构域编号 domain_id	1zumF02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	309 — Aldehyde Dehydrogenase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Aldehyde Dehydrogenase; Chain A, domain 2

结构域编号 domain_id	1zumG01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	605 — Aldehyde Dehydrogenase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aldehyde Dehydrogenase; Chain A, domain 1

结构域编号 domain_id	1zumG02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	309 — Aldehyde Dehydrogenase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Aldehyde Dehydrogenase; Chain A, domain 2

结构域编号 domain_id	1zumH01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	605 — Aldehyde Dehydrogenase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aldehyde Dehydrogenase; Chain A, domain 1

结构域编号 domain_id	1zumH02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	309 — Aldehyde Dehydrogenase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Aldehyde Dehydrogenase; Chain A, domain 2

结构域编号 domain_id	1zumI01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	605 — Aldehyde Dehydrogenase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aldehyde Dehydrogenase; Chain A, domain 1

结构域编号 domain_id	1zumI02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	309 — Aldehyde Dehydrogenase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Aldehyde Dehydrogenase; Chain A, domain 2

结构域编号 domain_id	1zumJ01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	605 — Aldehyde Dehydrogenase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aldehyde Dehydrogenase; Chain A, domain 1

结构域编号 domain_id	1zumJ02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	309 — Aldehyde Dehydrogenase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Aldehyde Dehydrogenase; Chain A, domain 2

结构域编号 domain_id	1zumK01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	605 — Aldehyde Dehydrogenase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aldehyde Dehydrogenase; Chain A, domain 1

结构域编号 domain_id	1zumK02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	309 — Aldehyde Dehydrogenase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Aldehyde Dehydrogenase; Chain A, domain 2

结构域编号 domain_id	1zumL01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	605 — Aldehyde Dehydrogenase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aldehyde Dehydrogenase; Chain A, domain 1

结构域编号 domain_id	1zumL02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	309 — Aldehyde Dehydrogenase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Aldehyde Dehydrogenase; Chain A, domain 2

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7. 引用文献 (1)

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晶胞边长 a length_a	95.873 Å
晶胞边长 b length_b	105.261 Å
晶胞边长 c length_c	162.672 Å
晶胞夹角 α angle_alpha	78.81 °
晶胞夹角 β angle_beta	81.95 °
晶胞夹角 γ angle_gamma	88.04 °
晶胞分子数 Z z_pdb	12

空间群 space_group	P 1
空间群编号 int_tables_number	1
晶系 crystal_system	—

分辨率 resolution	2.100 Å
最低分辨率 resolution_low	42.630 Å
R 因子 r_factor	0.2040
R_work r_work	0.2040
R_free r_free	0.2380

fit	/app/data/saxs_computation/zu/1zum/1zum.fit
pddf	/app/data/pr_computation/zu/1zum/1zum.pr.out
profile	/app/data/saxs_computation/zu/1zum/1zum.dat