2ahm

Crystal structure of SARS-CoV super complex of non-structural proteins: the hexadecamer

Method: X-RAY DIFFRACTION D_max: 129.4 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	2ahm
沉积日期 deposition_date	2005-07-28
结构标题 title	Crystal structure of SARS-CoV super complex of non-structural proteins: the hexadecamer
关键词 keywords	SARS-CoV, coronavirus, non-structural protein, nsp7, nsp8, super-complex, hexadecamer, Viral protein, Replication; Viral protein, Replication
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	37.74 Å
回转半径 Rg (电子) rg_electron	37.07 Å
零角强度 I(0) i0	188046000.00
分子量 molecular_weight	109510.0 kDa
排除体积 excluded_volume	137070 Å³
包络体积 envelope_volume	195560 Å³
水化壳体积 shell_volume	44012 Å³
包络直径 envelope_diameter	135.7 Å
壳层 Rg shell_rg	43.10 Å
包络 Rg envelope_rg	36.47 Å
形状 Rg shape_rg	37.13 Å
总 Rg total_rg	37.30 Å
总原子数 total_atoms	7633
残基数 n_residues	984
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	129.4 Å
Rg (实空间) rg_real	37.69 Å
Rg 误差 (实空间) rg_real_error	1.23 Å
I(0) (实空间) i0_real	1.8800e+08
I(0) 误差 (实空间) i0_real_error	3.0510e+06
Rg (倒空间) rg_reciprocal	37.73 Å
I(0) (倒空间) i0_reciprocal	188100000.0000
解质量估计 total_estimate	0.6739
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	52.4 Å
偏度 Skewness skewness	0.229
峰度 Kurtosis kurtosis	-0.433
角度范围 angular_range	— – 0.2100 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	32190000.0000
实空间数据点数 n_real_points	43
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.843; Stabil: 1.000; Sysdev: 0.080; Positv: 1.000; Valcen: 0.993; 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 (5)

Entity 1 polymer

描述 description	Replicase polyprotein 1ab, light chain
分子量 formula_weight	9688.3 kDa
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	7782

GPLGSSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINRLCEEMLDNRATLQ

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 BL21(DE3)

Entity 2 polymer

描述 description	Replicase polyprotein 1ab, heavy chain
分子量 formula_weight	22299.4 kDa
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	E,F,G,H

GPLGSAIASEFSSLPSYAAYATAQEAYEQAVANGDSEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVVPDYGTYKNTCDGNTFTYASALWEIQQVVDADSKIVQLSEINMDNSPNLAWPLIVTALRANSAVKLQ

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 BL21(DE3)

Entity 3 non-polymer

描述 description	GLYCEROL
分子量 formula_weight	92.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	5

Entity 4 non-polymer

描述 description	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 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	149

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6. 折叠分类 (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

结构域编号 domain_id	d2ahma1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.8 — immunoglobulin/albumin-binding domain-like
超家族 Superfamily superfamily	a.8.9 — Coronavirus NSP7-like
家族 Family family	a.8.9.1 — Coronavirus NSP7-like

结构域编号 domain_id	d2ahma2
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d2ahmb2
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.8 — immunoglobulin/albumin-binding domain-like
超家族 Superfamily superfamily	a.8.9 — Coronavirus NSP7-like
家族 Family family	a.8.9.1 — Coronavirus NSP7-like

结构域编号 domain_id	d2ahmb3
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d2ahmc2
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.8 — immunoglobulin/albumin-binding domain-like
超家族 Superfamily superfamily	a.8.9 — Coronavirus NSP7-like
家族 Family family	a.8.9.1 — Coronavirus NSP7-like

结构域编号 domain_id	d2ahmc3
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d2ahmd2
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.8 — immunoglobulin/albumin-binding domain-like
超家族 Superfamily superfamily	a.8.9 — Coronavirus NSP7-like
家族 Family family	a.8.9.1 — Coronavirus NSP7-like

结构域编号 domain_id	d2ahmd3
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d2ahme1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.302 — Coronavirus NSP8-like
超家族 Superfamily superfamily	d.302.1 — Coronavirus NSP8-like
家族 Family family	d.302.1.1 — Coronavirus NSP8-like

结构域编号 domain_id	d2ahmf_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.302 — Coronavirus NSP8-like
超家族 Superfamily superfamily	d.302.1 — Coronavirus NSP8-like
家族 Family family	d.302.1.1 — Coronavirus NSP8-like

结构域编号 domain_id	d2ahmg1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.302 — Coronavirus NSP8-like
超家族 Superfamily superfamily	d.302.1 — Coronavirus NSP8-like
家族 Family family	d.302.1.1 — Coronavirus NSP8-like

结构域编号 domain_id	d2ahmh1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.302 — Coronavirus NSP8-like
超家族 Superfamily superfamily	d.302.1 — Coronavirus NSP8-like
家族 Family family	d.302.1.1 — Coronavirus NSP8-like

CATH v4.4 (12 domains)

结构域编号 domain_id	2ahmA00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	8 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily	370 — nsp7 replicase

结构域编号 domain_id	2ahmB00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	8 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily	370 — nsp7 replicase

结构域编号 domain_id	2ahmC00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	8 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily	370 — nsp7 replicase

结构域编号 domain_id	2ahmD00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	8 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily	370 — nsp7 replicase

结构域编号 domain_id	2ahmE01
类 Class class	6 — Special
架构 Architecture architecture	10 — Helix non-globular
拓扑 Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	580 —

结构域编号 domain_id	2ahmE02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	3540 — Nsp8 replicase, head domain

结构域编号 domain_id	2ahmF01
类 Class class	6 — Special
架构 Architecture architecture	10 — Helix non-globular
拓扑 Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	580 —

结构域编号 domain_id	2ahmF02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	3540 — Nsp8 replicase, head domain

结构域编号 domain_id	2ahmG01
类 Class class	6 — Special
架构 Architecture architecture	10 — Helix non-globular
拓扑 Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	2820 —

结构域编号 domain_id	2ahmG02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	3540 — Nsp8 replicase, head domain

结构域编号 domain_id	2ahmH01
类 Class class	6 — Special
架构 Architecture architecture	10 — Helix non-globular
拓扑 Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	2820 —

结构域编号 domain_id	2ahmH02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	3540 — Nsp8 replicase, head domain

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7. 引用文献 (1)

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晶胞边长 a length_a	93.600 Å
晶胞边长 b length_b	94.000 Å
晶胞边长 c length_c	150.800 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	16

空间群 space_group	P 21 21 2
空间群编号 int_tables_number	18
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	0.2320
R_work r_work	0.2130
R_free r_free	0.2510

fit	/app/data/saxs_computation/ah/2ahm/2ahm.fit
pddf	/app/data/pr_computation/ah/2ahm/2ahm.pr.out
profile	/app/data/saxs_computation/ah/2ahm/2ahm.dat

Crystal structure of SARS-CoV super complex of non-structural proteins: the hexadecamer

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

5. 实体与聚合体信息 (5)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 water

6. 折叠分类 (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)