SAXSdb — 2gt7

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2gt7
沉积日期 deposition_date	2006-04-27
结构标题 title	Crystal structure of SARS coronavirus main peptidase at pH 6.0 in the space group P21
关键词 keywords	;cysteine peptidase, 3C-like, N-finger, chymotrypsin-like fold, long loop, alpha-helical domain, dimer, catalytic dyad, specificity pockets, 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	26.57 Å
回转半径 Rg (电子) rg_electron	25.55 Å
零角强度 I(0) i0	74779300.00
分子量 molecular_weight	66698.0 kDa
排除体积 excluded_volume	83103 Å³
包络体积 envelope_volume	100070 Å³
水化壳体积 shell_volume	32368 Å³
包络直径 envelope_diameter	87.0 Å
壳层 Rg shell_rg	33.05 Å
包络 Rg envelope_rg	25.70 Å
形状 Rg shape_rg	25.52 Å
总 Rg total_rg	26.43 Å
总原子数 total_atoms	4672
残基数 n_residues	602
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	83.0 Å
Rg (实空间) rg_real	26.44 Å
Rg 误差 (实空间) rg_real_error	0.59 Å
I(0) (实空间) i0_real	7.4780e+07
I(0) 误差 (实空间) i0_real_error	1.1760e+06
Rg (倒空间) rg_reciprocal	26.48 Å
I(0) (倒空间) i0_reciprocal	74780000.0000
解质量估计 total_estimate	0.9072
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	80.3 Å
偏度 Skewness skewness	0.145
峰度 Kurtosis kurtosis	-0.555
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	35950000.0000
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: 0.933; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.992

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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	3C-like proteinase
分子量 formula_weight	33876.6 kDa
EC 编号 ec_number	3.4.22.-
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	5354

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDTVYCPRHVICTAEDMLNPNYEDLLIRKSNHSFLVQAGNVQLRVIGHSMQNCLLRLKVDTSNPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNHTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGKFYGPFVDRQTAQAAGTDTTITLNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCAALKELLQNGMNGRTILGSTILEDEFTPFDVVRQCSGVTFQ

来源 Source

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

Entity 2 non-polymer

描述 description	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
分子量 formula_weight	195.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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	591

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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	d2gt7a_
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	d2gt7b_
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	2gt7A01
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	2gt7A02
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	2gt7A03
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	2gt7B01
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	2gt7B02
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	2gt7B03
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	52.389 Å
晶胞边长 b length_b	96.191 Å
晶胞边长 c length_c	67.911 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	102.91 °
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	1.820 Å
最低分辨率 resolution_low	40.000 Å
R 因子 r_factor	0.1723
R_work r_work	0.1699
R_free r_free	0.2169

fit	/app/data/saxs_computation/gt/2gt7/2gt7.fit
pddf	/app/data/pr_computation/gt/2gt7/2gt7.pr.out
profile	/app/data/saxs_computation/gt/2gt7/2gt7.dat

Crystal structure of SARS coronavirus main peptidase at pH 6.0 in the space group P21

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution