SAXSdb — 1r37

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1r37
沉积日期 deposition_date	2003-09-30
结构标题 title	Alcohol dehydrogenase from sulfolobus solfataricus complexed with NAD(H) and 2-ethoxyethanol
关键词 keywords	archaeon, zinc, NAD(H) dependent, holoform, 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	28.64 Å
回转半径 Rg (电子) rg_electron	28.24 Å
零角强度 I(0) i0	93461900.00
分子量 molecular_weight	76906.0 kDa
排除体积 excluded_volume	96549 Å³
包络体积 envelope_volume	111310 Å³
水化壳体积 shell_volume	33120 Å³
包络直径 envelope_diameter	97.0 Å
壳层 Rg shell_rg	35.22 Å
包络 Rg envelope_rg	28.42 Å
形状 Rg shape_rg	28.22 Å
总 Rg total_rg	28.92 Å
总原子数 total_atoms	5380
残基数 n_residues	694
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	93.8 Å
Rg (实空间) rg_real	28.71 Å
Rg 误差 (实空间) rg_real_error	0.65 Å
I(0) (实空间) i0_real	9.3460e+07
I(0) 误差 (实空间) i0_real_error	1.3090e+06
Rg (倒空间) rg_reciprocal	28.69 Å
I(0) (倒空间) i0_reciprocal	93460000.0000
解质量估计 total_estimate	0.8785
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	29.0 Å
偏度 Skewness skewness	0.430
峰度 Kurtosis kurtosis	-0.354
角度范围 angular_range	— – 0.2750 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	33410000.0000
实空间数据点数 n_real_points	56
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.864; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.936; Smooth: 0.888

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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	NAD-dependent alcohol dehydrogenase
分子量 formula_weight	37615.5 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	5584

MRAVRLVEIGKPLSLQEIGVPKPKGPQVLIKVEAAGVCHSDVHMRQGRFGNLRIVEDLGVKLPVTLGHEIAGKIEEVGDEVVGYSKGDLVAVNPWQGEGNCYYCRIGEEHLCDSPRWLGINFDGAYAEYVIVPHYKYMYKLRRLNAVEAAPLTCSGITTYRAVRKASLDPTKTLLVVGAGGGLGTMAVQIAKAVSGATIIGVDVREEAVEAAKRAGADYVINASMQDPLAEIRRITESKGVDAVIDLNNSEKTLSVYPKALAKQGKYVMVGLFGADLHYHAPLITLSEIQFVGSLVGNQSDFLGIMRLAEAGKVKPMITKTMKLEEANEAIDNLENFKAIGRQVLIP

来源 Source

来源生物 organism	Sulfolobus solfataricus
NCBI 分类编号 ncbi_taxonomy_id	2287
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 non-polymer

描述 description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
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	2-ETHOXYETHANOL
分子量 formula_weight	90.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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	204

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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	d1r37a1
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	d1r37a2
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	d1r37b1
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	d1r37b2
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	1r37A01
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	1r37A02
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	1r37B01
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	1r37B02
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 (3)

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晶胞边长 a length_a	131.064 Å
晶胞边长 b length_b	83.014 Å
晶胞边长 c length_c	68.674 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	96.46 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	—

分辨率 resolution	2.300 Å
最低分辨率 resolution_low	25.000 Å
R 因子 r_factor	—
R_work r_work	0.1930
R_free r_free	0.2250

fit	/app/data/saxs_computation/r3/1r37/1r37.fit
pddf	/app/data/pr_computation/r3/1r37/1r37.pr.out
profile	/app/data/saxs_computation/r3/1r37/1r37.dat

Alcohol dehydrogenase from sulfolobus solfataricus complexed with NAD(H) and 2-ethoxyethanol

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