SAXSdb — 1vlj

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1vlj
沉积日期 deposition_date	2004-07-28
结构标题 title	Crystal structure of NADH-dependent butanol dehydrogenase A (TM0820) from Thermotoga maritima at 1.78 A resolution
关键词 keywords	;TM0820, NADH-DEPENDENT BUTANOL DEHYDROGENASE A, STRUCTURAL GENOMICS, JCSG, PROTEIN STRUCTURE INITIATIVE, PSI, Joint Center for Structural Genomics, 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	27.70 Å
回转半径 Rg (电子) rg_electron	26.94 Å
零角强度 I(0) i0	117546000.00
分子量 molecular_weight	87641.0 kDa
排除体积 excluded_volume	110560 Å³
包络体积 envelope_volume	127110 Å³
水化壳体积 shell_volume	37933 Å³
包络直径 envelope_diameter	91.5 Å
壳层 Rg shell_rg	35.56 Å
包络 Rg envelope_rg	27.03 Å
形状 Rg shape_rg	26.94 Å
总 Rg total_rg	27.80 Å
总原子数 total_atoms	6176
残基数 n_residues	798
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	86.6 Å
Rg (实空间) rg_real	27.56 Å
Rg 误差 (实空间) rg_real_error	0.39 Å
I(0) (实空间) i0_real	1.1750e+08
I(0) 误差 (实空间) i0_real_error	1.4270e+06
Rg (倒空间) rg_reciprocal	27.61 Å
I(0) (倒空间) i0_reciprocal	117500000.0000
解质量估计 total_estimate	0.9034
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	34.9 Å
偏度 Skewness skewness	0.198
峰度 Kurtosis kurtosis	-0.466
角度范围 angular_range	— – 0.2850 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	48600000.0000
实空间数据点数 n_real_points	58
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.924; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.973

▶

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

▶

5. 实体与聚合体信息 (4)

Entity 1 polymer

描述 description	NADH-dependent butanol dehydrogenase
分子量 formula_weight	44875.7 kDa
EC 编号 ec_number	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	6669

MGSDKIHHHHHHMENFVFHNPTKIVFGRGTIPKIGEEIKNAGIRKVLFLYGGGSIKKNGVYDQVVDSLKKHGIEWVEVSGVKPNPVLSKVHEAVEVAKKEKVEAVLGVGGGSVVDSAKAVAAGALYEGDIWDAFIGKYQIEKALPIFDVLTISATGTEMNGNAVITNEKTKEKYGVSSKALYPKVSIIDPSVQFTLPKEQTVYGAVDAISHILEYYFDGSSPEISNEIAEGTIRTIMKMTERLIEKPDDYEARANLAWSATIALNGTMAVGRRGGEWACHRIEHSLSALYDIAHGAGLAIVFPAWMKYVYRKNPAQFERFAKKIFGFEGEGEELILKGIEAFKNWLKKVGAPVSLKDAGIPEEDIDKIVDNVMLLVEKNLKPKGASLGRIMVLEREDVREILKLAAK

来源 Source

来源生物 organism	Thermotoga maritima
NCBI 分类编号 ncbi_taxonomy_id	243274
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	FE (III) ION
分子量 formula_weight	55.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 3 non-polymer

描述 description	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
分子量 formula_weight	743.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 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	480

▼

6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1vlja1
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.22 — Dehydroquinate synthase-like
超家族 Superfamily superfamily	e.22.1 — Dehydroquinate synthase-like
家族 Family family	e.22.1.2 — Iron-containing alcohol dehydrogenase

结构域编号 domain_id	d1vlja2
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d1vljb1
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.22 — Dehydroquinate synthase-like
超家族 Superfamily superfamily	e.22.1 — Dehydroquinate synthase-like
家族 Family family	e.22.1.2 — Iron-containing alcohol dehydrogenase

结构域编号 domain_id	d1vljb2
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

CATH v4.4 (4 domains)

结构域编号 domain_id	1vljA01
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	1970 —

结构域编号 domain_id	1vljA02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1090 — Dehydroquinate synthase-like, alpha domain
同源超家族 H-superfamily homologous superfamily	10 — Dehydroquinate synthase-like - alpha domain

结构域编号 domain_id	1vljB01
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	1970 —

结构域编号 domain_id	1vljB02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1090 — Dehydroquinate synthase-like, alpha domain
同源超家族 H-superfamily homologous superfamily	10 — Dehydroquinate synthase-like - alpha domain

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	53.691 Å
晶胞边长 b length_b	129.699 Å
晶胞边长 c length_c	55.234 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	103.61 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	—

分辨率 resolution	1.780 Å
最低分辨率 resolution_low	49.600 Å
R 因子 r_factor	0.1447
R_work r_work	0.1422
R_free r_free	0.1926

fit	/app/data/saxs_computation/vl/1vlj/1vlj.fit
pddf	/app/data/pr_computation/vl/1vlj/1vlj.pr.out
profile	/app/data/saxs_computation/vl/1vlj/1vlj.dat

Crystal structure of NADH-dependent butanol dehydrogenase A (TM0820) from Thermotoga maritima at 1.78 A 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