SAXSdb — 8eev

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8eev
沉积日期 deposition_date	2022-09-07
结构标题 title	Venezuelan equine encephalitis virus-like particle in complex with Fab SKT-20
关键词 keywords	Venezuelan equine encephalitis virus, neutralizing antibody, VEEV, VIRUS LIKE PARTICLE-IMMUNE SYSTEM complex; VIRUS LIKE PARTICLE/IMMUNE SYSTEM
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	50.40 Å
回转半径 Rg (电子) rg_electron	50.30 Å
零角强度 I(0) i0	1200190000.00
分子量 molecular_weight	292340.0 kDa
排除体积 excluded_volume	366630 Å³
包络体积 envelope_volume	531440 Å³
水化壳体积 shell_volume	88923 Å³
包络直径 envelope_diameter	169.0 Å
壳层 Rg shell_rg	52.94 Å
包络 Rg envelope_rg	49.92 Å
形状 Rg shape_rg	50.26 Å
总 Rg total_rg	50.53 Å
总原子数 total_atoms	20640
残基数 n_residues	2659
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	165.0 Å
Rg (实空间) rg_real	50.30 Å
Rg 误差 (实空间) rg_real_error	1.66 Å
I(0) (实空间) i0_real	1.2000e+09
I(0) 误差 (实空间) i0_real_error	2.2400e+07
Rg (倒空间) rg_reciprocal	50.48 Å
I(0) (倒空间) i0_reciprocal	1200000000.0000
解质量估计 total_estimate	0.8868
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	58.5 Å
偏度 Skewness skewness	0.224
峰度 Kurtosis kurtosis	-0.462
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	62280000.0000
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: 0.879; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.893

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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	Coat protein
分子量 formula_weight	138662.5 kDa
来源方法 src_method	man
拷贝数 entity_count	6

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,F,G,J,K
原子数 atom_count	20640

MFPFQPMYPMQPMPYRNPFAAPRRPWFPRTDPFLAMQVQELTRSMANLTFKQRRDAPPEGPSAKKPKKEASQKQKGGGQGKKKKNQGKKKAKTGPPNPKAQNGNKKKTNKKPGKRQRMVMKLESDKTFPIMLEGKINGYACVVGGKLFRPMHVEGKIDNDVLAALKTKKASKYDLEYADVPQNMRADTFKYTHEKPQGYYSWHHGAVQYENGRFTVPKGVGAKGDSGRPILDNQGRVVAIVLGGVNEGSRTALSVVMWNEKGVTVKYTPENCEQWSLVTTMCLLANVTFPCAQPPICYDRKPAETLAMLSVNVDNPGYDELLEAAVKCPGRKRRSTEELFNEYKLTRPYMARCIRCAVGSCHSPIAIEAVKSDGHDGYVRLQTSSQYGLDSSGNLKGRTMRYDMHGTIKEIPLHQVSLYTSRPCHIVDGHGYFLLARCPAGDSITMEFKKDSVRHSCSVPYEVKFNPVGRELYTHPPEHGVEQACQVYAHDAQNRGAYVEMHLPGSEVDSSLVSLSGSSVTVTPPDGTSALVECECGGTKISETINKTKQFSQCTKKEQCRAYRLQNDKWVYNSDKLPKAAGATLKGKLHVPFLLADGKCTVPLAPEPMITFGFRSVSLKLHPKNPTYLITRQLADEPHYTHELISEPAVRNFTVTEKGWEFVWGNHPPKRFWAQETAPGNPHGLPHEVITHYYHRYPMSTILGLSICAAIATVSVAASTWLFCRSRVACLTPYRLTPNARIPFCLAVLCCARTARAETTWESLDHLWNNNQQMFWIQLLIPLAALIVVTRLLRCVCCVVPFLVMAGAAAPAYEHATTMPSQAGISYNTIVNRAGYAPLPISITPTKIKLIPTVNLEYVTCHYKTGMDSPAIKCCGSQECTPTYRPDEQCKVFTGVYPFMWGGAYCFCDTENTQVSKAYVMKSDDCLADHAEAYKAHTASVQAFLNITVGEHSIVTTVYVNGETPVNFNGVKITAGPLSTAWTPFDRKIVQYAGEIYNYDFPEYGAGQPGAFGDIQSRTVSSSDLYANTNLVLQRPKAGAIHVPYTQAPSGFEQWKKDKAPSLKFTAPFGCEIYTNPIRAENCAVGSIPLAFDIPDALFTRVSETPTLSAAECTLNECVYSSDFGGIATVKYSASKSGKCAVHVPSGTATLKEAAVELTEQGSATIHFSTANIHPEFRLQICTSYVTCKGDCHPPKDHIVTHPQYHAQTFTAAVSKTAWTWLTSLLGGSAVIIIIGLVLATIVAMYVLTNQKHN

来源 Source

来源生物 organism	Venezuelan equine encephalitis virus
NCBI 分类编号 ncbi_taxonomy_id	11036
宿主生物 host_organism	Homo sapiens

Entity 2 polymer

描述 description	Fab SKT20 heavy chain
分子量 formula_weight	25421.3 kDa
来源方法 src_method	man
拷贝数 entity_count	3

聚合体 Polymer

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

QVQVQESGPGLVKPSETLSLTCAVSSGSINDDSYYWTWIRQSPGKGLEWLGFIHGGTGKSFYNPSLESRVTISKDTSRNQFSLTLSSVSAADTAVYYCARSHFCSNTFCYGWFDVWGPGIRVTVSSASTKGPSVFPLAPSSRSTSESTAALGCLVKDYFPEPVTVSWNSGSLTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYVCNVNHKPSNTKVDKRVEIKTCGGLEVLFQ

来源 Source

来源生物 organism	Macaca fascicularis
NCBI 分类编号 ncbi_taxonomy_id	9541
宿主生物 host_organism	Homo sapiens

Entity 3 polymer

描述 description	Fab SKT20 light chain
分子量 formula_weight	23754.4 kDa
来源方法 src_method	man
拷贝数 entity_count	3

聚合体 Polymer

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

DVVMTQTPLSLPITPGEPASISCRSSQSLLHSNGNTYLHWYLQKPGQSPQLLIYGGSNRASGVPDRFSGSGSGTDFTLKISKVEAEDVGVYYCVQAIAFPWTFGQGTKVEIKRTVAAPSVFIFPPSEDQVKSGTVSVVCLLNNFYPREASVKWKVDGALKTGNSQESVTEQDSKDNTYSLSSTLTLSSTEYQSHKVYACEVTHQGLSSPVTKSFNRGEC

来源 Source

来源生物 organism	Macaca fascicularis
NCBI 分类编号 ncbi_taxonomy_id	9541
宿主生物 host_organism	Homo sapiens

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6. 折叠分类 (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

结构域编号 domain_id	8eevH01
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	8eevL01
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	8eevS01
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	8eevT01
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	8eevU01
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	8eevV01
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	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	3.60 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	28235

fit	/app/data/saxs_computation/ee/8eev/8eev.fit
pddf	/app/data/pr_computation/ee/8eev/8eev.pr.out
profile	/app/data/saxs_computation/ee/8eev/8eev.dat

Venezuelan equine encephalitis virus-like particle in complex with Fab SKT-20

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

6. 折叠分类 (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)