1lvn

CRYSTAL STRUCTURE OF E. COLI AMINE OXIDASE COMPLEXED WITH TRANYLCYPROMINE

Method: X-RAY DIFFRACTION D_max: 105.0 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	1lvn
沉积日期 deposition_date	2002-05-28
结构标题 title	CRYSTAL STRUCTURE OF E. COLI AMINE OXIDASE COMPLEXED WITH TRANYLCYPROMINE
关键词 keywords	Inhibitor complex, 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	33.87 Å
回转半径 Rg (电子) rg_electron	33.18 Å
零角强度 I(0) i0	394263000.00
分子量 molecular_weight	161340.0 kDa
排除体积 excluded_volume	202010 Å³
包络体积 envelope_volume	242600 Å³
水化壳体积 shell_volume	57921 Å³
包络直径 envelope_diameter	114.2 Å
壳层 Rg shell_rg	42.07 Å
包络 Rg envelope_rg	33.39 Å
形状 Rg shape_rg	33.15 Å
总 Rg total_rg	33.89 Å
总原子数 total_atoms	11371
残基数 n_residues	1436
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	105.0 Å
Rg (实空间) rg_real	33.71 Å
Rg 误差 (实空间) rg_real_error	0.67 Å
I(0) (实空间) i0_real	3.9430e+08
I(0) 误差 (实空间) i0_real_error	6.1230e+06
Rg (倒空间) rg_reciprocal	33.81 Å
I(0) (倒空间) i0_reciprocal	394300000.0000
解质量估计 total_estimate	0.8976
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	42.5 Å
偏度 Skewness skewness	0.179
峰度 Kurtosis kurtosis	-0.435
角度范围 angular_range	— – 0.2350 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	108500000.0000
实空间数据点数 n_real_points	48
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.915; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.938

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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 (4)

Entity 1 polymer

描述 description	Copper amine oxidase
分子量 formula_weight	81483.9 kDa
EC 编号 ec_number	1.4.3.6
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	12818

HGGEAHMVPMDKTLKEFGADVQWDDYAQLFTLIKDGAYVKVKPGAQTAIVNGQPLALQVPVVMKDNKAWVSDTFINDVFQSGLDQTFQVEKRPHPLNALTADEIKQAVEIVKASADFKPNTRFTEISLLPPDKEAVWAFALENKPVDQPRKADVIMLDGKHIIEAVVDLQNNKLLSWQPIKDAHGMVLLDDFASVQNIINNSEEFAAAVKKRGITDAKKVITTPLTVGYFDGKDGLKQDARLLKVISYLDVGDGNYWAHPIENLVAVVDLEQKKIVKIEEGPVVPVPMTARPFDGRDRVAPAVKPMQIIEPEGKNYTITGDMIHWRNWDFHLSMNSRVGPMISTVTYNDNGTKRKVMYEGSLGGMIVPYGDPDIGWYFKAYLDSGDYGMGTLTSPIARGKDAPSNAVLLNETIADYTGVPMEIPRAIAVFERYAGPEYKHQEMGQPNVSTERRELVVRWISTVGNYDYIFDWIFHENGTIGIDAGATGIEAVKGVKAKTMHDETAKDDTRYGTLIDHNIVGTTHQHIYNFRLDLDVDGENNSLVAMDPVVKPNTAGGPRTSTMQVNQYNIGNEQDAAQKFDPGTIRLLSNPNKENRMGNPVSYQIIPYAGGTHPVAKGAQFAPDEWIYHRLSFMDKQLWVTRYHPGERFPEGKYPNRSTHDTGLGQYSKDNESLDNTDAVVWMTTGTTHVARAEEWPIMPTEWVHTLLKPWNFFDETPTLGALKKDK

来源 Source

来源生物 organism	Escherichia coli
NCBI 分类编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	COPPER (II) ION
分子量 formula_weight	63.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 3 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	4

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	1447

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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	d1lvna1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.30 — Supersandwich
超家族 Superfamily superfamily	b.30.2 — Amine oxidase catalytic domain
家族 Family family	b.30.2.1 — Amine oxidase catalytic domain

结构域编号 domain_id	d1lvna2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.17 — Cystatin-like
超家族 Superfamily superfamily	d.17.2 — Amine oxidase N-terminal region
家族 Family family	d.17.2.1 — Amine oxidase N-terminal region

结构域编号 domain_id	d1lvna3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.17 — Cystatin-like
超家族 Superfamily superfamily	d.17.2 — Amine oxidase N-terminal region
家族 Family family	d.17.2.1 — Amine oxidase N-terminal region

结构域编号 domain_id	d1lvna4
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.82 — N domain of copper amine oxidase-like
超家族 Superfamily superfamily	d.82.1 — Copper amine oxidase, domain N
家族 Family family	d.82.1.1 — Copper amine oxidase, domain N

结构域编号 domain_id	d1lvnb1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.30 — Supersandwich
超家族 Superfamily superfamily	b.30.2 — Amine oxidase catalytic domain
家族 Family family	b.30.2.1 — Amine oxidase catalytic domain

结构域编号 domain_id	d1lvnb2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.17 — Cystatin-like
超家族 Superfamily superfamily	d.17.2 — Amine oxidase N-terminal region
家族 Family family	d.17.2.1 — Amine oxidase N-terminal region

结构域编号 domain_id	d1lvnb3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.17 — Cystatin-like
超家族 Superfamily superfamily	d.17.2 — Amine oxidase N-terminal region
家族 Family family	d.17.2.1 — Amine oxidase N-terminal region

结构域编号 domain_id	d1lvnb4
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.82 — N domain of copper amine oxidase-like
超家族 Superfamily superfamily	d.82.1 — Copper amine oxidase, domain N
家族 Family family	d.82.1.1 — Copper amine oxidase, domain N

CATH v4.4 (8 domains)

结构域编号 domain_id	1lvnA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	457 — Copper Amine Oxidase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Copper amine oxidase-like, N-terminal domain

结构域编号 domain_id	1lvnA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
同源超家族 H-superfamily homologous superfamily	40 —

结构域编号 domain_id	1lvnA03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	70 — Distorted Sandwich
拓扑 Topology topology	98 — Beta-galactosidase; Chain A, domain 5
同源超家族 H-superfamily homologous superfamily	20 — Copper amine oxidase, catalytic domain

结构域编号 domain_id	1lvnA04
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
同源超家族 H-superfamily homologous superfamily	40 —

结构域编号 domain_id	1lvnB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	457 — Copper Amine Oxidase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Copper amine oxidase-like, N-terminal domain

结构域编号 domain_id	1lvnB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
同源超家族 H-superfamily homologous superfamily	40 —

结构域编号 domain_id	1lvnB03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	70 — Distorted Sandwich
拓扑 Topology topology	98 — Beta-galactosidase; Chain A, domain 5
同源超家族 H-superfamily homologous superfamily	20 — Copper amine oxidase, catalytic domain

结构域编号 domain_id	1lvnB04
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
同源超家族 H-superfamily homologous superfamily	40 —

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7. 引用文献 (6)

;Medical implications from the crystal structure of a copper-containing amine oxidase complexed with the antidepressant drug tranylcypromine. ;

Febs Lett. (2004)

PMID: 15498552 · DOI: 10.1016/j.febslet.2004.09.031 PRIMARY

;Probing the catalytic mechanism of Escherichia coli amine oxidase using mutational variants and a reversible inhibitor as a substrate analogue. ;

BIOCHEM.J. (2002)

;The active site base controls cofactor reactivity in Escherichia coli amine oxidase: X-ray crystallographic studies with mutational variants. ;

Biochemistry (1999)

DOI: 10.1021/bi9900469

Visualization of dioxygen bound to copper during enzyme catalysis.

Science (1999)

DOI: 10.1126/science.286.5445.1724

Catalytic Mechanism of the Quinoenzyme Amine Oxidase from Escherichia Coli: Exploring the Reductive Half-Reaction.

Biochemistry (1997)

DOI: 10.1021/bi962205j

Crystal Structure of a Quinoenzyme: Copper Amine Oxidase of Escherichia Coli at 2 Angstroms Resolution.

Structure (1995)

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晶胞边长 a length_a	135.236 Å
晶胞边长 b length_b	166.482 Å
晶胞边长 c length_c	79.628 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.00 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

空间群 space_group	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	2.400 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.1850
R_work r_work	0.1850
R_free r_free	0.2290

fit	/app/data/saxs_computation/lv/1lvn/1lvn.fit
pddf	/app/data/pr_computation/lv/1lvn/1lvn.pr.out
profile	/app/data/saxs_computation/lv/1lvn/1lvn.dat