2ghw

Crystal structure of SARS spike protein receptor binding domain in complex with a neutralizing antibody, 80R

Method: X-RAY DIFFRACTION D_max: 171.7 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	2ghw
沉积日期 deposition_date	2006-03-27
结构标题 title	Crystal structure of SARS spike protein receptor binding domain in complex with a neutralizing antibody, 80R
关键词 keywords	SARS, S protein, neutralizing antibody, VIRUS-VIRAL PROTEIN-ANTIBIOTIC COMPLEX; VIRUS/VIRAL PROTEIN/ANTIBIOTIC
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	47.69 Å
回转半径 Rg (电子) rg_electron	48.70 Å
零角强度 I(0) i0	131613000.00
分子量 molecular_weight	93863.0 kDa
排除体积 excluded_volume	116990 Å³
包络体积 envelope_volume	160110 Å³
水化壳体积 shell_volume	30456 Å³
包络直径 envelope_diameter	169.5 Å
壳层 Rg shell_rg	45.13 Å
包络 Rg envelope_rg	48.11 Å
形状 Rg shape_rg	48.66 Å
总 Rg total_rg	48.69 Å
总原子数 total_atoms	6619
残基数 n_residues	842
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	171.7 Å
Rg (实空间) rg_real	48.66 Å
Rg 误差 (实空间) rg_real_error	2.97 Å
I(0) (实空间) i0_real	1.3160e+08
I(0) 误差 (实空间) i0_real_error	2.8020e+06
Rg (倒空间) rg_reciprocal	47.70 Å
I(0) (倒空间) i0_reciprocal	131400000.0000
解质量估计 total_estimate	0.6338
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	26.0 Å
偏度 Skewness skewness	0.435
峰度 Kurtosis kurtosis	-0.963
角度范围 angular_range	— – 0.1650 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	5641000.0000
实空间数据点数 n_real_points	34
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.086; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.061; Smooth: 0.916

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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	Spike glycoprotein
分子量 formula_weight	22883.8 kDa
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,C
原子数 atom_count	7089

MADPNITNLCPFGEVFNATKFPSVYAWERKKISNCVADYSVLYNSTFFSTFKCYGVSATKLNDLCFSNVYADSFVVKGDDVRQIAPGQTGVIADYNYKLPDDFMGCVLAWNTRNIDATSTGNYNYKYRYLRHGKLRPFERDISNVPFSPDGKPCTPPALNCYWPLNDYGFYTTTGIGYQPYRVVVLSFELLNAPATVSGLVPR

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	Spodoptera frugiperda

Entity 2 polymer

描述 description	anti-sars scFv antibody, 80R
分子量 formula_weight	26454.3 kDa
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	B,D

MAEVQLVQSGGGVVQPGKSLRLSCAASGFAFSSYAMHWVRQAPGKGLEWVAVISYDGSNKYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARDRSYYLDYWGQGTLVTVSSGGGGSGGGGSGGGGSETTLTQSPATLSLSPGERATLSCRASQSVRSNLAWYQQKPGQAPRPLIYDASTRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQRSNWPPTFGQGTKVEVKSGLVPR

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 3 non-polymer

描述 description	CHLORIDE ION
分子量 formula_weight	35.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	5

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	470

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6. 折叠分类 (SCOP + CATH) 13 domains

SCOP 2.08 (7 domains)

结构域编号 domain_id	d2ghwa_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.318 — SARS receptor-binding domain-like
超家族 Superfamily superfamily	d.318.1 — SARS receptor-binding domain-like
家族 Family family	d.318.1.1 — SARS receptor-binding domain-like

结构域编号 domain_id	d2ghwb1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.1 — Immunoglobulin
家族 Family family	b.1.1.1 — V set domains (antibody variable domain-like)

结构域编号 domain_id	d2ghwb2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.1 — Immunoglobulin
家族 Family family	b.1.1.1 — V set domains (antibody variable domain-like)

结构域编号 domain_id	d2ghwc_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.318 — SARS receptor-binding domain-like
超家族 Superfamily superfamily	d.318.1 — SARS receptor-binding domain-like
家族 Family family	d.318.1.1 — SARS receptor-binding domain-like

结构域编号 domain_id	d2ghwd1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.1 — Immunoglobulin
家族 Family family	b.1.1.1 — V set domains (antibody variable domain-like)

结构域编号 domain_id	d2ghwd2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.1 — Immunoglobulin
家族 Family family	b.1.1.1 — V set domains (antibody variable domain-like)

结构域编号 domain_id	d2ghwd3
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

CATH v4.4 (6 domains)

结构域编号 domain_id	2ghwA01
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	1840 — Spike protein, C-terminal core receptor binding subdomain

结构域编号 domain_id	2ghwB01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

结构域编号 domain_id	2ghwB02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

结构域编号 domain_id	2ghwC01
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	1840 — Spike protein, C-terminal core receptor binding subdomain

结构域编号 domain_id	2ghwD01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

结构域编号 domain_id	2ghwD02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

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7. 引用文献 (1)

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晶胞边长 a length_a	47.453 Å
晶胞边长 b length_b	175.902 Å
晶胞边长 c length_c	67.561 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	96.55 °
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	2.300 Å
最低分辨率 resolution_low	45.550 Å
R 因子 r_factor	0.2509
R_work r_work	0.2484
R_free r_free	0.2954

fit	/app/data/saxs_computation/gh/2ghw/2ghw.fit
pddf	/app/data/pr_computation/gh/2ghw/2ghw.pr.out
profile	/app/data/saxs_computation/gh/2ghw/2ghw.dat

Crystal structure of SARS spike protein receptor binding domain in complex with a neutralizing antibody, 80R

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 (4)

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 water

6. 折叠分类 (SCOP + CATH) 13 domains

SCOP 2.08 (7 domains)

CATH v4.4 (6 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)