2jbw

Crystal Structure of the 2,6-dihydroxy-pseudo-oxynicotine Hydrolase.

Method: X-RAY DIFFRACTION D_max: 154.2 Å Quality: REASONABLE

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	2jbw
沉积日期 deposition_date	2006-12-14
结构标题 title	Crystal Structure of the 2,6-dihydroxy-pseudo-oxynicotine Hydrolase.
关键词 keywords	;HYDROLASE, ALPHA/BETA HYDROLASE, META-CLEAVAGE PATHWAY, RETRO- FRIEDEL- CRAFTS ACYLATION, NICOTINE DEGRADATION, HYPOTHETICAL PROTEIN, PLASMID, CATALYTIC TRIAD, C-C BOND CLEAVAGE ;; HYDROLASE
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	47.03 Å
回转半径 Rg (电子) rg_electron	48.03 Å
零角强度 I(0) i0	394914000.00
分子量 molecular_weight	161870.0 kDa
排除体积 excluded_volume	200770 Å³
包络体积 envelope_volume	261410 Å³
水化壳体积 shell_volume	48732 Å³
包络直径 envelope_diameter	166.3 Å
壳层 Rg shell_rg	46.56 Å
包络 Rg envelope_rg	47.61 Å
形状 Rg shape_rg	48.05 Å
总 Rg total_rg	47.89 Å
总原子数 total_atoms	11246
残基数 n_residues	1390
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	154.2 Å
Rg (实空间) rg_real	47.84 Å
Rg 误差 (实空间) rg_real_error	1.95 Å
I(0) (实空间) i0_real	3.9490e+08
I(0) 误差 (实空间) i0_real_error	7.6820e+06
Rg (倒空间) rg_reciprocal	47.04 Å
I(0) (倒空间) i0_reciprocal	394500000.0000
解质量估计 total_estimate	0.7136
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	31.8 Å
偏度 Skewness skewness	0.558
峰度 Kurtosis kurtosis	-0.569
角度范围 angular_range	— – 0.1700 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	61930000.0000
实空间数据点数 n_real_points	35
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.536; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.626; Smooth: 0.045

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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 (3)

Entity 1 polymer

描述 description	2,6-DIHYDROXY-PSEUDO-OXYNICOTINE HYDROLASE
分子量 formula_weight	43861.5 kDa
EC 编号 ec_number	3.7.1.-
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	12210

ASMTGGQQMGRDPGMTVTSQVKPEDEMDNWGRLILDGVSYSDMVGARDRPKEITWFDYWMSLANEYEQEAERKVALGHDLSAGELLMSAALCAQYAQFLWFDERRQKGQARKVELYQKAAPLLSPPAERHELVVDGIPMPVYVRIPEGPGPHPAVIMLGGLESTKEESFQMENLVLDRGMATATFDGPGQGEMFEYKRIAGDYEKYTSAVVDLLTKLEAIRNDAIGVLGRSLGGNYALKSAACEPRLAACISWGGFSDLDYWDLETPLTKESWKYVSKVDTLEEARLHVHAALETRDVLSQIACPTYILHGVHDEVPLSFVDTVLELVPAEHLNLVVEKDGDHCCHNLGIRPRLEMADWLYDVLVAGKKVAPTMKGWPLEHHHHHH

来源 Source

来源生物 organism	ARTHROBACTER NICOTINOVORANS
NCBI 分类编号 ncbi_taxonomy_id	29320
宿主生物 host_organism	ESCHERICHIA COLI

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	4

Entity 3 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	964

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6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d2jbwa1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.69 — alpha/beta-Hydrolases
超家族 Superfamily superfamily	c.69.1 — alpha/beta-Hydrolases
家族 Family family	c.69.1.41 — 2,6-dihydropseudooxynicotine hydrolase-like

结构域编号 domain_id	d2jbwa2
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	d2jbwb1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.69 — alpha/beta-Hydrolases
超家族 Superfamily superfamily	c.69.1 — alpha/beta-Hydrolases
家族 Family family	c.69.1.41 — 2,6-dihydropseudooxynicotine hydrolase-like

结构域编号 domain_id	d2jbwb2
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	d2jbwc1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.69 — alpha/beta-Hydrolases
超家族 Superfamily superfamily	c.69.1 — alpha/beta-Hydrolases
家族 Family family	c.69.1.41 — 2,6-dihydropseudooxynicotine hydrolase-like

结构域编号 domain_id	d2jbwc2
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	d2jbwd1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.69 — alpha/beta-Hydrolases
超家族 Superfamily superfamily	c.69.1 — alpha/beta-Hydrolases
家族 Family family	c.69.1.41 — 2,6-dihydropseudooxynicotine hydrolase-like

结构域编号 domain_id	d2jbwd2
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 (8 domains)

结构域编号 domain_id	2jbwA01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1440 — de novo design (two linked rop proteins)
同源超家族 H-superfamily homologous superfamily	110 — acylaminoacyl peptidase

结构域编号 domain_id	2jbwA02
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	1820 — Alpha/Beta hydrolase fold, catalytic domain

结构域编号 domain_id	2jbwB01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1440 — de novo design (two linked rop proteins)
同源超家族 H-superfamily homologous superfamily	110 — acylaminoacyl peptidase

结构域编号 domain_id	2jbwB02
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	1820 — Alpha/Beta hydrolase fold, catalytic domain

结构域编号 domain_id	2jbwC01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1440 — de novo design (two linked rop proteins)
同源超家族 H-superfamily homologous superfamily	110 — acylaminoacyl peptidase

结构域编号 domain_id	2jbwC02
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	1820 — Alpha/Beta hydrolase fold, catalytic domain

结构域编号 domain_id	2jbwD01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1440 — de novo design (two linked rop proteins)
同源超家族 H-superfamily homologous superfamily	110 — acylaminoacyl peptidase

结构域编号 domain_id	2jbwD02
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	1820 — Alpha/Beta hydrolase fold, catalytic domain

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7. 引用文献 (1)

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晶胞边长 a length_a	90.570 Å
晶胞边长 b length_b	57.020 Å
晶胞边长 c length_c	152.697 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	103.35 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

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	2.100 Å
最低分辨率 resolution_low	30.000 Å
R 因子 r_factor	0.1830
R_work r_work	0.1810
R_free r_free	0.2380

fit	/app/data/saxs_computation/jb/2jbw/2jbw.fit
pddf	/app/data/pr_computation/jb/2jbw/2jbw.pr.out
profile	/app/data/saxs_computation/jb/2jbw/2jbw.dat