2bvh

Crystal structure of 6-hydoxy-D-nicotine oxidase from Arthrobacter nicotinovorans. Crystal Form 2 (P21)

Method: X-RAY DIFFRACTION D_max: 163.8 Å Quality: GOOD

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	2bvh
沉积日期 deposition_date	2005-06-28
结构标题 title	Crystal structure of 6-hydoxy-D-nicotine oxidase from Arthrobacter nicotinovorans. Crystal Form 2 (P21)
关键词 keywords	AUTOFLAVINYLATION, ENANTIOMERIC SUBSTRATES, FLAVOENZYMES, NICOTINE DEGRADATION, OXIDASE; OXIDASE
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	45.86 Å
回转半径 Rg (电子) rg_electron	46.45 Å
零角强度 I(0) i0	595123000.00
分子量 molecular_weight	196280.0 kDa
排除体积 excluded_volume	243590 Å³
包络体积 envelope_volume	309660 Å³
水化壳体积 shell_volume	59509 Å³
包络直径 envelope_diameter	173.2 Å
壳层 Rg shell_rg	46.45 Å
包络 Rg envelope_rg	46.36 Å
形状 Rg shape_rg	46.43 Å
总 Rg total_rg	46.51 Å
总原子数 total_atoms	13808
残基数 n_residues	1812
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	163.8 Å
Rg (实空间) rg_real	46.26 Å
Rg 误差 (实空间) rg_real_error	2.29 Å
I(0) (实空间) i0_real	5.9510e+08
I(0) 误差 (实空间) i0_real_error	1.2830e+07
Rg (倒空间) rg_reciprocal	45.86 Å
I(0) (倒空间) i0_reciprocal	594800000.0000
解质量估计 total_estimate	0.8282
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	53.0 Å
偏度 Skewness skewness	0.558
峰度 Kurtosis kurtosis	0.024
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	60320000.0000
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: 0.745; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.927; Smooth: 0.600

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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 (2)

Entity 1 polymer

描述 description	6-HYDROXY-D-NICOTINE OXIDASE
分子量 formula_weight	48918.1 kDa
EC 编号 ec_number	1.5.3.6
突变 mutation	YES
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	13808

MVSSKLATPLSIQGEVIYPDDSGFDAIANIWDGRHLQRPSLIARCLSAGDVAKSVRYACDNGLEISVRSGGHNPNGYATNDGGIVLDLRLMNSIHIDTAGSRARIGGGVISGDLVKEAAKFGLAAVTGMHPKVGFCGLALNGGVGFLTPKYGLASDNILGATLVTATGDVIYCSDDERPELFWAVRGAGPNFGVVTEVEVQLYELPRKMLAGFITWAPSVSELAGLLTSLLDALNEMADHIYPSVFVGVDENRAPSVTVCVGHLGGLDIAERDIARLRGLGRTVSDSIAVRSYDEVVALNAEVGSFEDGMSNLWIDREIAMPNARFAEAIAGNLDKFVSEPASGGSVKLEIEGMPFGNPKRTPARHRDAMGVLALAEWSGAAPGSEKYPELARELDAALLRAGVTTSGFGLLNNNSEVTAEMVAEVYKPEVYSRLAAVKREYDPENRFRHNYNIDPEGS

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	FLAVIN-ADENINE DINUCLEOTIDE
分子量 formula_weight	785.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

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6. 折叠分类 (SCOP + CATH) 20 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d2bvha1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.58 — Ferredoxin-like
超家族 Superfamily superfamily	d.58.32 — FAD-linked oxidases, C-terminal domain
家族 Family family	d.58.32.5 — 6-hydroxy-d-nicotine oxidase

结构域编号 domain_id	d2bvha2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.145 — FAD-binding/transporter-associated domain-like
超家族 Superfamily superfamily	d.145.1 — FAD-binding/transporter-associated domain-like
家族 Family family	d.145.1.1 — FAD-linked oxidases, N-terminal domain

结构域编号 domain_id	d2bvhb1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.58 — Ferredoxin-like
超家族 Superfamily superfamily	d.58.32 — FAD-linked oxidases, C-terminal domain
家族 Family family	d.58.32.5 — 6-hydroxy-d-nicotine oxidase

结构域编号 domain_id	d2bvhb2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.145 — FAD-binding/transporter-associated domain-like
超家族 Superfamily superfamily	d.145.1 — FAD-binding/transporter-associated domain-like
家族 Family family	d.145.1.1 — FAD-linked oxidases, N-terminal domain

结构域编号 domain_id	d2bvhc1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.58 — Ferredoxin-like
超家族 Superfamily superfamily	d.58.32 — FAD-linked oxidases, C-terminal domain
家族 Family family	d.58.32.5 — 6-hydroxy-d-nicotine oxidase

结构域编号 domain_id	d2bvhc2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.145 — FAD-binding/transporter-associated domain-like
超家族 Superfamily superfamily	d.145.1 — FAD-binding/transporter-associated domain-like
家族 Family family	d.145.1.1 — FAD-linked oxidases, N-terminal domain

结构域编号 domain_id	d2bvhd1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.58 — Ferredoxin-like
超家族 Superfamily superfamily	d.58.32 — FAD-linked oxidases, C-terminal domain
家族 Family family	d.58.32.5 — 6-hydroxy-d-nicotine oxidase

结构域编号 domain_id	d2bvhd2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.145 — FAD-binding/transporter-associated domain-like
超家族 Superfamily superfamily	d.145.1 — FAD-binding/transporter-associated domain-like
家族 Family family	d.145.1.1 — FAD-linked oxidases, N-terminal domain

CATH v4.4 (12 domains)

结构域编号 domain_id	2bvhA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	43 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2

结构域编号 domain_id	2bvhA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	465 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	2bvhA03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	462 — Vanillyl-alcohol Oxidase; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	2bvhB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	43 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2

结构域编号 domain_id	2bvhB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	465 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	2bvhB03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	462 — Vanillyl-alcohol Oxidase; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	2bvhC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	43 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2

结构域编号 domain_id	2bvhC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	465 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	2bvhC03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	462 — Vanillyl-alcohol Oxidase; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	2bvhD01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	43 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2

结构域编号 domain_id	2bvhD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	465 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	2bvhD03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	462 — Vanillyl-alcohol Oxidase; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	20 —

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7. 引用文献 (1)

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晶胞边长 a length_a	103.320 Å
晶胞边长 b length_b	90.940 Å
晶胞边长 c length_c	104.440 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	100.31 °
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	2.900 Å
最低分辨率 resolution_low	44.300 Å
R 因子 r_factor	0.2740
R_work r_work	0.2740
R_free r_free	0.2970

fit	/app/data/saxs_computation/bv/2bvh/2bvh.fit
pddf	/app/data/pr_computation/bv/2bvh/2bvh.pr.out
profile	/app/data/saxs_computation/bv/2bvh/2bvh.dat

Crystal structure of 6-hydoxy-D-nicotine oxidase from Arthrobacter nicotinovorans. Crystal Form 2 (P21)

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