8dry

Product structure of SARS-CoV-2 Mpro C145A mutant in complex with nsp12-nsp13 (C12) cut site sequence

Method: X-RAY DIFFRACTION D_max: 233.1 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	8dry
沉积日期 deposition_date	2022-07-21
结构标题 title	Product structure of SARS-CoV-2 Mpro C145A mutant in complex with nsp12-nsp13 (C12) cut site sequence
关键词 keywords	Viral protease, SARS-CoV-2, VIRAL PROTEIN; VIRAL PROTEIN
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	81.06 Å
回转半径 Rg (电子) rg_electron	82.79 Å
零角强度 I(0) i0	2300380000.00
分子量 molecular_weight	401150.0 kDa
排除体积 excluded_volume	499900 Å³
包络体积 envelope_volume	764210 Å³
水化壳体积 shell_volume	87594 Å³
包络直径 envelope_diameter	306.3 Å
壳层 Rg shell_rg	61.48 Å
包络 Rg envelope_rg	81.43 Å
形状 Rg shape_rg	82.77 Å
总 Rg total_rg	82.49 Å
总原子数 total_atoms	28128
残基数 n_residues	3644
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	233.1 Å
Rg (实空间) rg_real	78.59 Å
Rg 误差 (实空间) rg_real_error	1.48 Å
I(0) (实空间) i0_real	2.2590e+09
I(0) 误差 (实空间) i0_real_error	4.8060e+07
Rg (倒空间) rg_reciprocal	75.78 Å
I(0) (倒空间) i0_reciprocal	2268000000.0000
解质量估计 total_estimate	0.7417
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	3
主峰位置 r_peak_primary	49.1 Å
偏度 Skewness skewness	0.490
峰度 Kurtosis kurtosis	-0.753
角度范围 angular_range	— – 0.0950 Å⁻¹
当前正则化参数 α current_alpha	0.0474
最高正则化参数 α highest_alpha	51720000.0000
实空间数据点数 n_real_points	20
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.586; Stabil: 0.971; Sysdev: 1.000; Positv: 1.000; Valcen: 0.657; Smooth: 0.070

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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	Fusion protein of 3C-like proteinase nsp5 and nsp12-nsp13 (C12) cut site
分子量 formula_weight	33850.6 kDa
EC 编号 ec_number	3.4.22.69,2.7.7.48
来源方法 src_method	man
拷贝数 entity_count	12

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F,G,H,I,J,K,L
原子数 atom_count	28308

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSAGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCPHTVLQ

来源 Source

来源生物 organism	Severe acute respiratory syndrome coronavirus 2
通用名 common_name	SARS-CoV-2, 2019-nCoV
NCBI 分类编号 ncbi_taxonomy_id	2697049
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	DI(HYDROXYETHYL)ETHER
分子量 formula_weight	106.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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	159

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6. 折叠分类 (SCOP + CATH) 21 domains

CATH v4.4 (21 domains)

结构域编号 domain_id	8dryA01
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	8dryA02
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	8dryB01
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	8dryB02
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	8dryC01
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	8dryD01
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	8dryE01
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	8dryE02
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	8dryF01
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	8dryF02
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	8dryG01
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	8dryG02
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	8dryH01
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	8dryH02
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	8dryI01
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	8dryJ01
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	8dryJ02
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	8dryK01
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	8dryK02
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	8dryL01
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	8dryL02
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	67.329 Å
晶胞边长 b length_b	107.923 Å
晶胞边长 c length_c	277.248 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.73 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	24

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	2.490 Å
最低分辨率 resolution_low	65.230 Å
R 因子 r_factor	0.1956
R_work r_work	0.1942
R_free r_free	0.2641

fit	/app/data/saxs_computation/dr/8dry/8dry.fit
pddf	/app/data/pr_computation/dr/8dry/8dry.pr.out
profile	/app/data/saxs_computation/dr/8dry/8dry.dat

Product structure of SARS-CoV-2 Mpro C145A mutant in complex with nsp12-nsp13 (C12) cut site sequence

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