SAXSdb — 1h2b

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1h2b
沉积日期 deposition_date	2002-08-02
结构标题 title	Crystal Structure of the Alcohol Dehydrogenase from the Hyperthermophilic Archaeon Aeropyrum pernix at 1.65A Resolution
关键词 keywords	OXIDOREDUCTASE, ARCHAEA, HYPERTHERMOPHILE, ALCOHOL DEHYDROGENASE OXIDOREDUCTASE, ZINC; 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	30.24 Å
回转半径 Rg (电子) rg_electron	29.47 Å
零角强度 I(0) i0	95351900.00
分子量 molecular_weight	77333.0 kDa
排除体积 excluded_volume	97033 Å³
包络体积 envelope_volume	121070 Å³
水化壳体积 shell_volume	33671 Å³
包络直径 envelope_diameter	92.4 Å
壳层 Rg shell_rg	37.31 Å
包络 Rg envelope_rg	29.07 Å
形状 Rg shape_rg	29.50 Å
总 Rg total_rg	30.10 Å
总原子数 total_atoms	5415
残基数 n_residues	687
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	94.5 Å
Rg (实空间) rg_real	30.21 Å
Rg 误差 (实空间) rg_real_error	0.49 Å
I(0) (实空间) i0_real	9.5350e+07
I(0) 误差 (实空间) i0_real_error	1.2750e+06
Rg (倒空间) rg_reciprocal	30.23 Å
I(0) (倒空间) i0_reciprocal	95350000.0000
解质量估计 total_estimate	0.9050
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	29.1 Å
偏度 Skewness skewness	0.203
峰度 Kurtosis kurtosis	-0.742
角度范围 angular_range	— – 0.2600 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	43670000.0000
实空间数据点数 n_real_points	53
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.945; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.976; Smooth: 0.949

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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	ALCOHOL DEHYDROGENASE
分子量 formula_weight	39620.7 kDa
EC 编号 ec_number	1.1.1.1
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	A,B
原子数 atom_count	6104

MRIEQDFSQSLGVERLKAARLHEYNKPLRIEDVDYPRLEGRFDVIVRIAGAGVCHTDLHLVQGMWHELLQPKLPYTLGHENVGYIEEVAEGVEGLEKGDPVILHPAVTDGTCLACRAGEDMHCENLEFPGLNIDGGFAEFMRTSHRSVIKLPKDISREKLVEMAPLADAGITAYRAVKKAARTLYPGAYVAIVGVGGLGHIAVQLLKVMTPATVIALDVKEEKLKLAERLGADHVVDARRDPVKQVMELTRGRGVNVAMDFVGSQATVDYTPYLLGRMGRLIIVGYGGELRFPTIRVISSEVSFEGSLVGNYVELHELVTLALQGKVRVEVDIHKLDEINDVLERLEKGEVLGRAVLIP

来源 Source

来源生物 organism	AEROPYRUM PERNIX
NCBI 分类编号 ncbi_taxonomy_id	56636
宿主生物 host_organism	Escherichia coli DH5[alpha]

Entity 2 non-polymer

描述 description	OCTANOIC ACID (CAPRYLIC ACID)
分子量 formula_weight	144.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 3 non-polymer

描述 description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE (ACIDIC FORM)
分子量 formula_weight	663.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 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	5

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	660

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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	d1h2ba1
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	d1h2ba2
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	d1h2bb1
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	d1h2bb2
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 (4 domains)

结构域编号 domain_id	1h2bA01
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	1h2bA02
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	1h2bB01
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	1h2bB02
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

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7. 引用文献 (2)

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晶胞边长 a length_a	100.661 Å
晶胞边长 b length_b	103.186 Å
晶胞边长 c length_c	67.521 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	8

空间群 space_group	P 21 21 2
空间群编号 int_tables_number	18
晶系 crystal_system	—

分辨率 resolution	1.620 Å
最低分辨率 resolution_low	15.000 Å
R 因子 r_factor	0.1683
R_work r_work	0.1676
R_free r_free	0.2033

fit	/app/data/saxs_computation/h2/1h2b/1h2b.fit
pddf	/app/data/pr_computation/h2/1h2b/1h2b.pr.out
profile	/app/data/saxs_computation/h2/1h2b/1h2b.dat

Crystal Structure of the Alcohol Dehydrogenase from the Hyperthermophilic Archaeon Aeropyrum pernix at 1.65A Resolution

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