SAXSdb — 8xa1

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8xa1
沉积日期 deposition_date	2023-12-01
最后修订 last_revision	2025-04-30
结构标题 title	Portal vertex capsomer of VZV B-capsid
关键词 keywords	VZV, capsid structure, VIRAL PROTEIN; 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	66.31 Å
回转半径 Rg (电子) rg_electron	66.51 Å
零角强度 I(0) i0	3257460000.00
分子量 molecular_weight	482940.0 kDa
排除体积 excluded_volume	605060 Å³
包络体积 envelope_volume	968240 Å³
水化壳体积 shell_volume	122400 Å³
包络直径 envelope_diameter	216.3 Å
壳层 Rg shell_rg	65.40 Å
包络 Rg envelope_rg	65.29 Å
形状 Rg shape_rg	66.51 Å
总 Rg total_rg	66.48 Å
总原子数 total_atoms	33981
残基数 n_residues	4496
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	234.0 Å
Rg (实空间) rg_real	66.40 Å
Rg 误差 (实空间) rg_real_error	2.42 Å
I(0) (实空间) i0_real	3.2580e+09
I(0) 误差 (实空间) i0_real_error	6.7840e+07
Rg (倒空间) rg_reciprocal	66.17 Å
I(0) (倒空间) i0_reciprocal	3256000000.0000
解质量估计 total_estimate	0.8649
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	58.5 Å
偏度 Skewness skewness	0.225
峰度 Kurtosis kurtosis	-0.690
角度范围 angular_range	— – 0.1200 Å⁻¹
当前正则化参数 α current_alpha	0.0022
最高正则化参数 α highest_alpha	448400000.0000
实空间数据点数 n_real_points	25
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.806; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.972; Smooth: 0.849

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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	Major capsid protein
分子量 formula_weight	149896.5 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	33981

PAGIIPTGNVLSTIEVCAHRCIFDFFKQIRSDDNSLYSAQFDILLGTYCNTLNFVRFLELGLSVACICTKFPELAYVRDGVIQFEVQQPMIARDGPHPVDQPVHNYMVKRIHKRSLSAAFAIASEALSLLSNTYVDGTEIDSSLRIRAIQQMARNLRTVLDSFERGTADQLLGVLLEKAPPLSLLSPINKFQPEGHLNRVARAALLSDLKRRVCADMFFMTRHAREPRLISAYLSDMVSCTQPSVMVSRITHTNTRGRQVDGVLVTTATLKRQLLQGILQIDDTAADVPVTVLNGANLVTALVMGKAVRSLDDVGRHLLDMQEEQLENARVPADLVIVGDKLVFLEALERRVYQATRVAYPLIGNIDITFIMPMGVFQANSMDRYTRHAGDFSTVSEQDPRQFPPQGIFFYNKDGILTQLTLRDAMGTICHSSLLDVEATLVALRQQHLDRQCYFGVYVAEGTEDTLDVQMGRFMETWADMMPHHPHWVNEHLTILQFIAPSNPRLRFELNPAFDFFVAPGDVDLPGPQRPPEAMPTVNATLRIINGNIPVPLCPISFRDCRGTQLGLGRHTMTPATIKAVKDTFEDRAYPTIFYMLEAVIHGNERNFCALLRLLTQCIRGYWEQSHRVAFVNNFHMLMYITTYLGNGELPEVCINIYRDLLQHVRALRQTITDFTIQGEGHNGETSEALNNILTDDTFIAPILWDCDALIYRDEAARDRLPAIRVSGRNGYQALHFVDMAGHNFQRRDNVLIHGRPVRGDTGQAIPITPHHDREWGILSKIYYYIVIPAFSRGSCCTMGVRYDRLYPALQAVIVPEIPADEEAPTTPEDPRHPLHAHQLVPNSLNVYFHNAHLTVDGDALLTLQELMGDMAERTTAILVSSAPDAGAATATTRNMRIYDGALYHGLIMMAYQAYDETIATGTFFYPVPVNPLFACPEHLASLRGMTNARRVLAKMVPPIPPFLGANHHATIRQPVAYHVTHSKSDFNTLTYSLLGGYFKFTPISLTHQLRTGFHPGIAFTVVRQDRFATEQLLYAERASESYFVGQIQVHHHDAIGGVNFTLTQPRAHVDLGVGYTAVCATAALRCPLTDMGNTAQNLFFSRGGVPMLHDNVTESLRRITASGGRLNPTEPLPIFGGLRPATSAGIARGQASVCEFVAMPVSTDLQYFRTACNPRGRASGMLYMGDRDADIEAIMFDHTQSDVAYTDRATLNPWASQKHSYGDRLYNGTYNLTGASPIYSPCFKFFTPAEVNTNCNTLDRLLMEAKAVASQSSTDTEYQFKRPPGSTEMTQDPCGLFQEAYPPLCSSDAAMLRTAHAGETGADEVHLAQYLIRDASPLRGCLPL

来源 Source

来源生物 organism	Human alphaherpesvirus 3
NCBI 分类编号 ncbi_taxonomy_id	10335
宿主生物 host_organism	Homo sapiens

Entity 2 polymer

描述 description	major capsid protein
分子量 formula_weight	144341.4 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	C

IPAGIIPTGNVLSTIEVCIFFRFLELGLSVACICTKFPELAYVRDGVIQFEVQQPMIARDGPHPVDQPVHNYMVKRIHKRSLSAAFAIASEALSLLSNTYVDGTEIDSSLRIRAIQQMARNLRTVSDSFERGTADQLLGVLLEKAPPLSLLSPINKFQPEGHLNRVARAALLSDLKRRVCADMFFMTRHAREPRLISAYLSDMVSCTQPSVMVSRITHTNTRGRQVDGVLVTTATLKRQLLQGILQIDDTAADVPVTYGEMVLQGTNLVTALVMGKAVRNARVPADLVIVGDKLVFLEALERRVYQATRVAYPLIGNIDITFIMPMGVFQANSMDRYTRHAGDFSTVSEQDPRQFPPQGIFFYNKDGILTQLTLRDAMGTICHSSLLDVEATLVALRQQHLDRQCYFGVYVAEGTEDTLDVQMGRFMETWADMMPHHPHWVNEHLTILQFIAPSNPRLRFELNPAFDFFVAPGDVDLPGPQRPPEAMPTVNATLRIINGNIPVPLCPISFRDCRGTQLGLGRHTMTPATIKAVKDTFEDRAYPTIFYMLEAVIHGNERNFCALLRLLTQCIRGYWEQSHRVAFVNNFHMLMYITTYLGNGELPEVCINIYRDLLQHVRALRQTITDFTIQGEGHNGETSEALNNILTDDTFIAPILWDCDALIYRDEAARDRLPAIRVSGRNGYQALHFVDMAGHNFQRRDNVLIHGRPVRGDTGQAIPITPHHDREWGILSKIYYYIVIPAFSRGSCCTMGVRYDRLYPALQAVIVPEIPADEEAPTTPEDPRHPLHAHQLVPNSLNVYFHNAHLTVDGDALLTLQELMGDMAERTTAILVSSAPDAGAATATTRNMRIYDGALYHGLIMMAYQAYDETIATGTFFYPVPVNPLFACPEHLASLRGMTNARRVLAKMVPPIPPFLGANHHATIRQPVAYHVTHSKSDFNTLTYSLLGGYFKFTPISLTHQLRTGFHPGIAFTVVRQDRFATEQLLYAERASESYFVGQIQVHHHDAIGGVNFTLTQPRAHVDLGVGYTAVCATAALRCPLTDMGNTAQNLFFSRGGVPMLHDNVTESLRRITASGGRLNPTEPLPIFGGLRPATSAGIARGQASVCEFVAMPVSTDLQYFRTACNPRGRASGMLYMGDRDADIEAIMFDHTQSDVAYTDRATLNPWASQKHSYGDRLYNGTYNLTGASPIYSPCFKFFTPAEVNTNCNTLDRLLMEAKAVASQSSTDTEYQFKRPPGSTEMTQDPCGLFQEAYPPLCSSDAAMLRTAHAGETGADEVHLAQYLIRDASPLRGCLPL

来源 Source

来源生物 organism	Human alphaherpesvirus 3
NCBI 分类编号 ncbi_taxonomy_id	10335
宿主生物 host_organism	Homo sapiens

Entity 3 polymer

描述 description	Tri2A
分子量 formula_weight	32225.6 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	G,I

AMPFEIEVLLPGELSPAETSALQKCEGKIITFSTLRHRASLVDIALSSYYINGAPPDTLSLLEAYRMRFAAVITRVIPGKLLAHAIGVGTPTPGLFIQNTSPVDLCNGDYICLLPPVFGSADSIRLDSVGLEIVFPLTIPQTLMREIIAKVVARAVEDLNPDPDLNVLYYNGARLSLVADVQQLASDAAIRTLVLNLMFSINEGCLLILALIPRLLALGYVNALLQMQSVTREAAQLIHPEAPMLMRRLPIYETISSWISTSSRLGDTLGTRAILRVCVFDGPSTVHPGDRTAVIQV

来源 Source

来源生物 organism	Human alphaherpesvirus 3
NCBI 分类编号 ncbi_taxonomy_id	10335
宿主生物 host_organism	Homo sapiens

Entity 4 polymer

描述 description	Tri2B
分子量 formula_weight	33420.5 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	P,R

AMPFEIEVLLPGEISPAETSALQKCEGKIITFSTLRHRASLVDIALSSYYINGAPPDTLSLLEAYRMRFAAVITRVIPGKLLAHAIGVGTPTPGLFIQNTSPVDLCNGDYICLLPPVFGSADEIRLDSVGLEIVFPLTIPQTLMREIIAKVVARAVERTAAGRTPGELPGADVICYNGRRYELETNLQHRDGSDAAIRTLVLNLMFSINEGTTLILTLITRLLVQGAHDGYVNLLIQTANCVRETGQPMPRIQDGHRRFPIYEAISSWISTSSRLGDTLGTRAILRVCVFDGPSTVHPGDRTAVIQV

来源 Source

来源生物 organism	Human alphaherpesvirus 3
NCBI 分类编号 ncbi_taxonomy_id	10335
宿主生物 host_organism	Homo sapiens

Entity 5 polymer

描述 description	Tri1
分子量 formula_weight	38719.1 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	Y,d

AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAIVINRMNNIQINPTSIGNPQTIRLPLNNFKSTTQLIQQVSLTDFFRPDIEHAGSTVLILRHPTDLPHLARHRAPPGRQTERLAEAWGQLLEASESGCARAYVTSLSFIAACRAEEYTDKQAAEANRTAIVSAYGCSRMGARLIRFSECLRAMVQCHVFPHRFISFFGSLLEYTIQDNLCNITAVAKGPQEAARTDKTSTRRVTANIPACVFWDVDKDLHLSADGLKHVFLVFVYTQRRQREGVRLHLALSQLNEQCFGRGIGFLLGARICMYAAYTLIGTIPSESVRYTRRMERFGGYNVPTIWLEGVVWGGTNTWNECY

来源 Source

来源生物 organism	Human alphaherpesvirus 3
NCBI 分类编号 ncbi_taxonomy_id	10335
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	4.800 Å
最低分辨率 resolution_low	— Å
R 因子 r_factor	—
R_work r_work	—
R_free r_free	—

分辨率 resolution	4.80 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	25531

fit	/app/data/saxs_computation/xa/8xa1/8xa1.fit
pddf	/app/data/pr_computation/xa/8xa1/8xa1.pr.out
profile	/app/data/saxs_computation/xa/8xa1/8xa1.dat

Portal vertex capsomer of VZV B-capsid

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

冷冻电镜 EM 3D

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 polymer

聚合体 Polymer

来源 Source

Entity 4 polymer

聚合体 Polymer

来源 Source

Entity 5 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)