1uk3

Crystal structure of SARS Coronavirus Main Proteinase (3CLpro) At pH7.6

Method: X-RAY DIFFRACTION D_max: 82.8 Å Quality: EXCELLENT

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	1uk3
沉积日期 deposition_date	2003-08-14
结构标题 title	Crystal structure of SARS Coronavirus Main Proteinase (3CLpro) At pH7.6
关键词 keywords	anti-parallel b-barrel, anti-parallel a-helices, Hydrolase; 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	26.49 Å
回转半径 Rg (电子) rg_electron	25.48 Å
零角强度 I(0) i0	74711500.00
分子量 molecular_weight	66655.0 kDa
排除体积 excluded_volume	83024 Å³
包络体积 envelope_volume	100770 Å³
水化壳体积 shell_volume	32656 Å³
包络直径 envelope_diameter	88.7 Å
壳层 Rg shell_rg	32.98 Å
包络 Rg envelope_rg	25.53 Å
形状 Rg shape_rg	25.46 Å
总 Rg total_rg	26.33 Å
总原子数 total_atoms	4669
残基数 n_residues	603
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	82.8 Å
Rg (实空间) rg_real	26.35 Å
Rg 误差 (实空间) rg_real_error	0.60 Å
I(0) (实空间) i0_real	7.4710e+07
I(0) 误差 (实空间) i0_real_error	1.1000e+06
Rg (倒空间) rg_reciprocal	26.39 Å
I(0) (倒空间) i0_reciprocal	74710000.0000
解质量估计 total_estimate	0.9061
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	80.0 Å
偏度 Skewness skewness	0.145
峰度 Kurtosis kurtosis	-0.547
角度范围 angular_range	— – 0.3000 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	35650000.0000
实空间数据点数 n_real_points	61
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.931; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.985

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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)

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6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d1uk3a_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.47 — Trypsin-like serine proteases
超家族 Superfamily superfamily	b.47.1 — Trypsin-like serine proteases
家族 Family family	b.47.1.4 — Viral cysteine protease of trypsin fold

结构域编号 domain_id	d1uk3b_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.47 — Trypsin-like serine proteases
超家族 Superfamily superfamily	b.47.1 — Trypsin-like serine proteases
家族 Family family	b.47.1.4 — Viral cysteine protease of trypsin fold

CATH v4.4 (6 domains)

结构域编号 domain_id	1uk3A01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	10 — Thrombin, subunit H
同源超家族 H-superfamily homologous superfamily	10 — Trypsin-like serine proteases

结构域编号 domain_id	1uk3A02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	10 — Thrombin, subunit H
同源超家族 H-superfamily homologous superfamily	10 — Trypsin-like serine proteases

结构域编号 domain_id	1uk3A03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1840 — main proteinase (3clpro) structure, domain 3
同源超家族 H-superfamily homologous superfamily	10 — main proteinase (3clpro) structure, domain 3

结构域编号 domain_id	1uk3B01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	10 — Thrombin, subunit H
同源超家族 H-superfamily homologous superfamily	10 — Trypsin-like serine proteases

结构域编号 domain_id	1uk3B02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	10 — Thrombin, subunit H
同源超家族 H-superfamily homologous superfamily	10 — Trypsin-like serine proteases

结构域编号 domain_id	1uk3B03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1840 — main proteinase (3clpro) structure, domain 3
同源超家族 H-superfamily homologous superfamily	10 — main proteinase (3clpro) structure, domain 3

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7. 引用文献 (1)

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晶胞边长 a length_a	49.294 Å
晶胞边长 b length_b	97.033 Å
晶胞边长 c length_c	67.781 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	101.92 °
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	2.400 Å
最低分辨率 resolution_low	50.000 Å
R 因子 r_factor	0.2400
R_work r_work	0.2290
R_free r_free	0.2450

描述 description	3C-like proteinase
分子量 formula_weight	33876.6 kDa
EC 编号 ec_number	3.4.24.-
来源方法 src_method	man
拷贝数 entity_count	2

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	4783

Crystal structure of SARS Coronavirus Main Proteinase (3CLpro) At pH7.6

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

5. 实体与聚合体信息 (2)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 water

6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

CATH v4.4 (6 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)

来源生物 organism	SARS coronavirus
NCBI 分类编号 ncbi_taxonomy_id	227859
宿主生物 host_organism	Escherichia coli BL21(DE3)

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	114

fit	/app/data/saxs_computation/uk/1uk3/1uk3.fit
pddf	/app/data/pr_computation/uk/1uk3/1uk3.pr.out
profile	/app/data/saxs_computation/uk/1uk3/1uk3.dat