SAXSdb — 8r8k

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8r8k
沉积日期 deposition_date	2023-11-29
结构标题 title	XBB-4 Fab in complex with SARS-CoV-2 BA.2.12.1 Spike Glycoprotein
关键词 keywords	;SARS-CoV-2, Spike, Glycoprotein, Coronavirus, antibody, Fab, XBB.1.5, therapeutic, complex, neutralising, RBD, receptor binding domain, convalescent sera, viral protein, immune system, XBB-4, BA.2.12.1, omicron variant, virus, BA.2.86 ;; VIRAL PROTEIN
实验方法 method	ELECTRON MICROSCOPY

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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	29.83 Å
回转半径 Rg (电子) rg_electron	29.83 Å
零角强度 I(0) i0	52303100.00
分子量 molecular_weight	56760.0 kDa
排除体积 excluded_volume	70956 Å³
包络体积 envelope_volume	92010 Å³
水化壳体积 shell_volume	27415 Å³
包络直径 envelope_diameter	120.4 Å
壳层 Rg shell_rg	34.35 Å
包络 Rg envelope_rg	30.83 Å
形状 Rg shape_rg	29.75 Å
总 Rg total_rg	30.52 Å
总原子数 total_atoms	4005
残基数 n_residues	515
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	113.0 Å
Rg (实空间) rg_real	30.17 Å
Rg 误差 (实空间) rg_real_error	1.20 Å
I(0) (实空间) i0_real	5.2300e+07
I(0) 误差 (实空间) i0_real_error	8.6980e+05
Rg (倒空间) rg_reciprocal	30.02 Å
I(0) (倒空间) i0_reciprocal	52300000.0000
解质量估计 total_estimate	0.7779
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	27.7 Å
偏度 Skewness skewness	0.641
峰度 Kurtosis kurtosis	-0.024
角度范围 angular_range	— – 0.2650 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	11930000.0000
实空间数据点数 n_real_points	54
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.546; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.494; Smooth: 0.976

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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	Spike glycoprotein,Fibritin
分子量 formula_weight	142729.2 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	4005

MFVFLVLLPLVSSQCVNLITRTQSYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLGRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIRGNEVSQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVGGNYNYQYRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGFNCYFPLRSYGFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTQTKSHRRARSVASQSIIAYTMSLGAENLVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGRSLEVLFQGPGHHHHHHHHGSAWSHPQFEKGGGSGGGSGGSAWSHPQFEK

来源 Source

来源生物 organism	Tequatrovirus T4
NCBI 分类编号 ncbi_taxonomy_id	10665
宿主生物 host_organism	Homo sapiens

Entity 2 polymer

描述 description	XBB-4 Fab Heavy chain
分子量 formula_weight	24755.7 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	H

EVQLVQSGGGLVKPGGSLRLSCAASGFSFTNAWMNWVRQAPGKGLEWVGRIKSKADGGTTDYAAPVKGKFTISRDDSKNTLYLQMNSLKTEDTAIYYCTSDVYDFSTGFGQRDDFDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDK

来源 Source

来源生物 organism	Homo sapiens
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 3 polymer

描述 description	XBB-4 Fab Light chain
分子量 formula_weight	23185.8 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	L

DIVMTQSPSSLSASVGDRVTITCRASQSISYFLNWYQQKPGKAPKLLISAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSYSSLITFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

来源 Source

来源生物 organism	Homo sapiens
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

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7. 引用文献 (1)

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晶胞边长 a length_a	1.000 Å
晶胞边长 b length_b	1.000 Å
晶胞边长 c length_c	1.000 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	—

空间群 space_group	P 1
空间群编号 int_tables_number	1
晶系 crystal_system	—

分辨率 resolution	3.41 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	61333

fit	/app/data/saxs_computation/r8/8r8k/8r8k.fit
pddf	/app/data/pr_computation/r8/8r8k/8r8k.pr.out
profile	/app/data/saxs_computation/r8/8r8k/8r8k.dat

XBB-4 Fab in complex with SARS-CoV-2 BA.2.12.1 Spike Glycoprotein

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

冷冻电镜 EM 3D

5. 实体与聚合体信息 (3)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 polymer

聚合体 Polymer

来源 Source

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)