SAXSdb — 1kb0

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1kb0
沉积日期 deposition_date	2001-11-05
结构标题 title	Crystal Structure of Quinohemoprotein Alcohol Dehydrogenase from Comamonas testosteroni
关键词 keywords	beta-propeller fold, cytochrome c, 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	24.78 Å
回转半径 Rg (电子) rg_electron	23.80 Å
零角强度 I(0) i0	88678900.00
分子量 molecular_weight	73900.0 kDa
排除体积 excluded_volume	92194 Å³
包络体积 envelope_volume	103330 Å³
水化壳体积 shell_volume	34317 Å³
包络直径 envelope_diameter	83.5 Å
壳层 Rg shell_rg	32.66 Å
包络 Rg envelope_rg	24.17 Å
形状 Rg shape_rg	23.76 Å
总 Rg total_rg	24.79 Å
总原子数 total_atoms	5222
残基数 n_residues	669
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	84.2 Å
Rg (实空间) rg_real	24.60 Å
Rg 误差 (实空间) rg_real_error	0.65 Å
I(0) (实空间) i0_real	8.8680e+07
I(0) 误差 (实空间) i0_real_error	1.2840e+06
Rg (倒空间) rg_reciprocal	24.65 Å
I(0) (倒空间) i0_reciprocal	88680000.0000
解质量估计 total_estimate	0.7808
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	3
主峰位置 r_peak_primary	32.1 Å
偏度 Skewness skewness	0.167
峰度 Kurtosis kurtosis	-0.476
角度范围 angular_range	— – 0.3200 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	35980000.0000
实空间数据点数 n_real_points	64
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.730; Stabil: 0.986; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

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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 (7)

Entity 1 polymer

描述 description	quinohemoprotein alcohol dehydrogenase
分子量 formula_weight	73438.5 kDa
EC 编号 ec_number	1.1.99.-
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	6286

TGPAAQAAAAVQRVDGDFIRANAARTPDWPTIGVDYAETRYSRLDQINAANVKDLGLAWSYNLESTRGVEATPVVVDGIMYVSASWSVVHAIDTRTGNRIWTYDPQIDRSTGFKGCCDVVNRGVALWKGKVYVGAWDGRLIALDAATGKEVWHQNTFEGQKGSLTITGAPRVFKGKVIIGNGGAEYGVRGYITAYDAETGERKWRWFSVPGDPSKPFEDESMKRAARTWDPSGKWWEAGGGGTMWDSMTFDAELNTMYVGTGNGSPWSHKVRSPKGGDNLYLASIVALDPDTGKYKWHYQETPGDNWDYTSTQPMILADIKIAGKPRKVILHAPKNGFFFVLDRTNGKFISAKNFVPVNWASGYDKHGKPIGIAAARDGSKPQDAVPGPYGAHNWHPMSFNPQTGLVYLPAQNVPVNLMDDKKWEFNQAGPGKPQSGTGWNTAKFFNAEPPKSKPFGRLLAWDPVAQKAAWSVEHVSPWNGGTLTTAGNVVFQGTADGRLVAYHAATGEKLWEAPTGTGVVAAPSTYMVDGRQYVSVAVGWGGVYGLAARATERQGPGTVYTFVVGGKARMPEFVAQRTGQLLQGVKYDPAKVEAGTMLYVANCVFCHGVPGVDRGGNIPNLGYMDASYIENLPNFVFKGPAMVRGMPDFTGKLSGDDVESLKAFIQGTADAIRPKP

Entity 2 non-polymer

描述 description	CALCIUM ION
分子量 formula_weight	40.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 3 non-polymer

描述 description	HEME C
分子量 formula_weight	618.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 4 non-polymer

描述 description	TETRAHYDROFURAN-2-CARBOXYLIC ACID
分子量 formula_weight	116.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 non-polymer

描述 description	PYRROLOQUINOLINE QUINONE
分子量 formula_weight	330.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 6 non-polymer

描述 description	GLYCEROL
分子量 formula_weight	92.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 7 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	1016

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6. 折叠分类 (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d1kb0a1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.3 — Cytochrome c
超家族 Superfamily superfamily	a.3.1 — Cytochrome c
家族 Family family	a.3.1.6 — Quinoprotein alcohol dehydrogenase, C-terminal domain

结构域编号 domain_id	d1kb0a2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.70 — 8-bladed beta-propeller
超家族 Superfamily superfamily	b.70.1 — Quinoprotein alcohol dehydrogenase-like
家族 Family family	b.70.1.1 — Quinoprotein alcohol dehydrogenase-like

CATH v4.4 (2 domains)

结构域编号 domain_id	1kb0A01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	140 — 8 Propeller
拓扑 Topology topology	10 — Methanol Dehydrogenase; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Quinoprotein alcohol dehydrogenase-like superfamily

结构域编号 domain_id	1kb0A02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	760 — Cytochrome Bc1 Complex; Chain D, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Cytochrome c-like domain

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7. 引用文献 (2)

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晶胞边长 a length_a	97.920 Å
晶胞边长 b length_b	74.331 Å
晶胞边长 c length_c	92.332 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	105.67 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

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	1.440 Å
最低分辨率 resolution_low	29.630 Å
R 因子 r_factor	0.1600
R_work r_work	0.1600
R_free r_free	0.1880

fit	/app/data/saxs_computation/kb/1kb0/1kb0.fit
pddf	/app/data/pr_computation/kb/1kb0/1kb0.pr.out
profile	/app/data/saxs_computation/kb/1kb0/1kb0.dat

Crystal Structure of Quinohemoprotein Alcohol Dehydrogenase from Comamonas testosteroni

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution