8zer

Crystal structure of the complex of Wuhan SARS-CoV-2 RBD (319-541) with P2C5 nanobody

Method: X-RAY DIFFRACTION D_max: 145.3 Å Quality: GOOD

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	8zer
沉积日期 deposition_date	2024-05-06
结构标题 title	Crystal structure of the complex of Wuhan SARS-CoV-2 RBD (319-541) with P2C5 nanobody
关键词 keywords	SARS-CoV-2, Spike glycoprotein fragment, complex with nanobody, VIRAL PROTEIN, VIRAL PROTEIN-IMMUNE SYSTEM complex; VIRAL PROTEIN/IMMUNE SYSTEM
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	50.55 Å
回转半径 Rg (电子) rg_electron	50.29 Å
零角强度 I(0) i0	474844000.00
分子量 molecular_weight	176880.0 kDa
排除体积 excluded_volume	219280 Å³
包络体积 envelope_volume	340680 Å³
水化壳体积 shell_volume	58079 Å³
包络直径 envelope_diameter	160.2 Å
壳层 Rg shell_rg	51.94 Å
包络 Rg envelope_rg	48.61 Å
形状 Rg shape_rg	50.25 Å
总 Rg total_rg	50.49 Å
总原子数 total_atoms	12457
残基数 n_residues	1569
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	145.3 Å
Rg (实空间) rg_real	50.53 Å
Rg 误差 (实空间) rg_real_error	1.26 Å
I(0) (实空间) i0_real	4.7480e+08
I(0) 误差 (实空间) i0_real_error	8.7600e+06
Rg (倒空间) rg_reciprocal	50.55 Å
I(0) (倒空间) i0_reciprocal	474900000.0000
解质量估计 total_estimate	0.8412
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	75.0 Å
偏度 Skewness skewness	0.111
峰度 Kurtosis kurtosis	-0.771
角度范围 angular_range	— – 0.1550 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	21190000.0000
实空间数据点数 n_real_points	32
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.988; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.967; Smooth: 0.000

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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	Spike protein S1
分子量 formula_weight	26647.9 kDa
来源方法 src_method	man
拷贝数 entity_count	5

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B,C,E,G,I
原子数 atom_count	12475

RVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFGSHHHHHHHHHH

来源 Source

来源生物 organism	Severe acute respiratory syndrome coronavirus 2
NCBI 分类编号 ncbi_taxonomy_id	2697049
宿主生物 host_organism	Cricetulus griseus

Entity 2 polymer

描述 description	Nanobody P2C5
分子量 formula_weight	16046.5 kDa
来源方法 src_method	man
拷贝数 entity_count	5

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,D,F,H,J

EVQLVESGGGSVQAGGSLRLSCVASGYTYCSYDMSWYRQAPGKEREFVSIIRRDGSTAYTDAVKGRFAISRDNAKNTLYLQMNSLEPEDTAMYYCKSWACSSGEYLYQGDWGQGTQVTVSSAAAEQKLISEEDLNGAAHHHHHHGS

来源 Source

来源生物 organism	Camelus bactrianus
NCBI 分类编号 ncbi_taxonomy_id	9837
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 3 branched

描述 description	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	586.5 kDa
来源方法 src_method	man
拷贝数 entity_count	2

Entity 4 branched

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	424.4 kDa
来源方法 src_method	man
拷贝数 entity_count	2

Entity 5 branched

描述 description	;beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-mannopyranose-(1-4)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	1276.2 kDa
来源方法 src_method	man
拷贝数 entity_count	1

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7. 引用文献 (1)

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晶胞边长 a length_a	72.483 Å
晶胞边长 b length_b	177.458 Å
晶胞边长 c length_c	209.861 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	20

空间群 space_group	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	3.100 Å
最低分辨率 resolution_low	45.170 Å
R 因子 r_factor	0.2248
R_work r_work	0.2218
R_free r_free	0.2827

fit	/app/data/saxs_computation/ze/8zer/8zer.fit
pddf	/app/data/pr_computation/ze/8zer/8zer.pr.out
profile	/app/data/saxs_computation/ze/8zer/8zer.dat

Crystal structure of the complex of Wuhan SARS-CoV-2 RBD (319-541) with P2C5 nanobody

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 (5)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 branched

Entity 4 branched

Entity 5 branched

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)