SAXSdb — 9no1

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	9no1
沉积日期 deposition_date	2025-03-07
结构标题 title	Cryo-ET map of the VZV capsid vertex (5-fold axis).
关键词 keywords	Varicella-zoster virus, capsid, cryo-ET, cryo-FIB, VIRUS; VIRUS
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	95.69 Å
回转半径 Rg (电子) rg_electron	95.73 Å
零角强度 I(0) i0	28818300000.00
分子量 molecular_weight	1451400.0 kDa
排除体积 excluded_volume	1816600 Å³
包络体积 envelope_volume	3490100 Å³
水化壳体积 shell_volume	297880 Å³
包络直径 envelope_diameter	358.4 Å
壳层 Rg shell_rg	94.38 Å
包络 Rg envelope_rg	95.34 Å
形状 Rg shape_rg	95.75 Å
总 Rg total_rg	95.65 Å
总原子数 total_atoms	102113
残基数 n_residues	13253
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	253.5 Å
Rg (实空间) rg_real	91.85 Å
Rg 误差 (实空间) rg_real_error	0.73 Å
I(0) (实空间) i0_real	2.7520e+10
I(0) 误差 (实空间) i0_real_error	5.6600e+08
Rg (倒空间) rg_reciprocal	94.73 Å
I(0) (倒空间) i0_reciprocal	28720000000.0000
解质量估计 total_estimate	0.9143
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	110.9 Å
偏度 Skewness skewness	0.219
峰度 Kurtosis kurtosis	-0.625
角度范围 angular_range	— – 0.0800 Å⁻¹
当前正则化参数 α current_alpha	0.9629
最高正则化参数 α highest_alpha	2314000000.0000
实空间数据点数 n_real_points	17
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.001; Oscil: 1.000; Stabil: 0.966; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; 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 (7)

Entity 1 polymer

描述 description	ORF40
分子量 formula_weight	155145.4 kDa
来源方法 src_method	nat
拷贝数 entity_count	7

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,D,F,H,J,L
原子数 atom_count	102113

MTTVSCPANVITTTESDRIAGLFNIPAGIIPTGNVLSTIEVCAHRCIFDFFKQIRSDDNSLYSAQFDILLGTYCNTLNFVRFLELGLSVACICTKFPELAYVRDGVIQFEVQQPMIARDGPHPVDQPVHNYMVKRIHKRSLSAAFAIASEALSLLSNTYVDGTEIDSSLRIRAIQQMARNLRTVLDSFERGTADQLLGVLLEKAPPLSLLSPINKFQPEGHLNRVARAALLSDLKRRVCADMFFMTRHAREPRLISAYLSDMVSCTQPSVMVSRITHTNTRGRQVDGVLVTTATLKRQLLQGILQIDDTAADVPVTYGEMVLQGTNLVTALVMGKAVRGMDDVARHLLDITDPNTLNIPSIPPQSNSDSTTAGLPVNARVPADLVIVGDKLVFLEALERRVYQATRVAYPLIGNIDITFIMPMGVFQANSMDRYTRHAGDFSTVSEQDPRQFPPQGIFFYNKDGILTQLTLRDAMGTICHSSLLDVEATLVALRQQHLDRQCYFGVYVAEGTEDTLDVQMGRFMETWADMMPHHPHWVNEHLTILQFIAPSNPRLRFELNPAFDFFVAPGDVDLPGPQRPPEAMPTVNATLRIINGNIPVPLCPISFRDCRGTQLGLGRHTMTPATIKAVKDTFEDRAYPTIFYMLEAVIHGNERNFCALLRLLTQCIRGYWEQSHRVAFVNNFHMLMYITTYLGNGELPEVCINIYRDLLQHVRALRQTITDFTIQGEGHNGETSEALNNILTDDTFIAPILWDCDALIYRDEAARDRLPAIRVSGRNGYQALHFVDMAGHNFQRRDNVLIHGRPVRGDTGQGIPITPHHDREWGILSKIYYYIVIPAFSRGSCCTMGVRYDRLYPALQAVIVPEIPADEEAPTTPEDPRHPLHAHQLVPNSLNVYFHNAHLTVDGDALLTLQELMGDMAERTTAILVSSAPDAGAATATTRNMRIYDGALYHGLIMMAYQAYDETIATGTFFYPVPVNPLFACPEHLASLRGMTNARRVLAKMVPPIPPFLGANHHATIRQPVAYHVTHSKSDFNTLTYSLLGGYFKFTPISLTHQLRTGFHPGIAFTVVRQDRFATEQLLYAERASESYFVGQIQVHHHDAIGGVNFTLTQPRAHVDLGVGYTAVCATAALRCPLTDMGNTAQNLFFSRGGVPMLHDNVTESLRRITASGGRLNPTEPLPIFGGLRPATSAGIARGQASVCEFVAMPVSTDLQYFRTACNPRGRASGMLYMGDRDADIEAIMFDHTQSDVAYTDRATLNPWASQKHSYGDRLYNGTYNLTGASPIYSPCFKFFTPAEVNTNCNTLDRLLMEAKAVASQSSTDTEYQFKRPPGSTEMTQDPCGLFQEAYPPLCSSDAAMLRTAHAGETGADEVHLAQYLIRDASPLRGCLPLPR

Entity 2 polymer

描述 description	Small capsomere-interacting protein
分子量 formula_weight	24440.1 kDa
来源方法 src_method	nat
拷贝数 entity_count	6

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	C,E,G,I,K,M

MTQPASSRVVFDPSNPTTFSVEAIAAYTPVALIRLLNASGPLQPGHRVDIADARSIYTVGAAASAARARANHNANTIRRTAMFAETDPMTWLRPTVGLKRTFNPRIIRPQPPNPSMSLGISGPTILPQKTQSADQSALQQPAALAFSGSSPQHPPPQTTSASVGQQQHVVSGSSGQQPQQGAQSSTVQPTTGSPPAAQGVPQSTPPPTQNTPQGGKGQTLSHTGQSGNASRSRRV

Entity 3 polymer

描述 description	ORF20
分子量 formula_weight	54028.2 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

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

MGSQPTNSHFTLNEQTLCGTNISLLGNNRFIQIGNGLHMTYAPGFFGNWSRDLTIGPRFGGLNKQPIHVPPKRTETASIQVTPRSIVINRMNNIQINPTSIGNPQVTIRLPLNNFKSTTQLIQQVSLTDFFRPDIEHAGSIVLILRHPSDMIGEANTLTQAGRDPDVLLEGLRNLFNACTAPWTVGEGGGLRAYVTSLSFIAACRAEEYTDKQAADANRTAIVSAYGCSRMETRLIRFSECLRAMVQCHVFPHRFISFFGSLLEYTIQDNLCNITAVAKGPQEAARTDKTSTRRVTANIPACVFWDVDKDLHLSADGLKHVFLVFVYTQRRQREGVRLHLALSQLNEQCFGRGIGFLLGRIRAENAAWGTEGVANTHQPYNTRALPLVQLSNDPTSPRCSIGEITGVNWNLARQRLYQWTGDFRGLPTQLSCMYAAYTLIGTIPSESVRYTRRMERFGGYNVPTIWLEGVVWGGTNTWNECYY

Entity 4 polymer

描述 description	ORF41
分子量 formula_weight	34421.9 kDa
来源方法 src_method	nat
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	O,P,R,S

MAMPFEIEVLLPGELSPAETSALQKCEGKIITFSTLRHRASLVDIALSSYYINGAPPDTLSLLEAYRMRFAAVITRVIPGKLLAHAIGVGTPTPGLFIQNTSPVDLCNGDYICLLPPVFGSADSIRLDSVGLEIVFPLTIPQTLMREIIAKVVARAVERTAAGAQILPHEVLRGADVICYNGRRYELETNLQHRDGSDAAIRTLVLNLMFSINEGCLLLLALIPTLLVQGAHDGYVNLLIQTANCVRETGQLINIPPMPRIQDGHRRFPIYETISSWISTSSRLGDTLGTRAILRVCVFDGPSTVHPGDRTAVIQV

Entity 5 polymer

描述 description	ORF43
分子量 formula_weight	73978.4 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

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

MEAHLANETKHALWHNDHTKGLLHVVIPNAGLIAAGIDPALLILKKPGQRFKVEVQTRYHATGQCEPWCQVFAAYIPDNALTNLLIPKTEPFVSHVFSATHNSGGLILSLPVYLSPGLFFDAFNVVAIRINTGNRKHRDICIMYAELIPNGTRYFADGQRVLLLCKQLIAYIRCTPRLASSIKIYAEHMVAAMGESHTSNGDNIGPVSSIIDLDRQLTSGGIDDSPAETRIQENNRDVLELIKRAVNIVNSRHPVRPSSSRVASGLLQSAKGHGAQTSNTDPINNGSFDGVLEPPGQGRFTGKKNNSSASIPPLQDVLLFTPASTEPQSLMEWFDICYAQLVSGDTPADFWKRRPLSIVPRHYAESPSPLIVVSYNGSSAWGGRITGSPILYHSAQAIIDAACINARVDNPQSLHVTARQELVARLPFLANVLNNQTPLPAFKPGAEMFLNQVFKQACVTSLTQGLITELQTNPTLQQLMEYDIADSSQTVIDEIVARTPDLIQTIVSVLTEMSMDAFYNSSLMYAVLAYLSSVYTRPQGGGYIPYLHASFPCWLGNRSIYLFDYYNSGGEILKLSKVPVPVALEKVGIGNSTQLRGKFIRSADIVDIGICSKYLPGQCYAYICLGFNQQLQSILVLPGGFAACFCITDTLQAALPASLIGPILDRFCFSIPNPHK

Entity 6 polymer

描述 description	ORF34
分子量 formula_weight	65253.9 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

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

MTARYGFGSISFPNKCGIFLSTTKNFIAPNFPIHYWTAPAFELRGRMNPDLEKNTLTLKNAAAVAALDNLRGETITLPTEIDRRLKPLEEQLTRMAKVLDSLETAAAEAEEADAQSEECTRTEIIRNESIHPEVQIAKNDAPLQYDTNFQVDFITLVYLGRARGNNSPGIVFGPWYRTLQERLVLDRPVAARGVDCKDGRISRTFMNTTVTCLQSAGRMYVGDRAYSAFECAVLCLYLMYRTSNSVHEPQVSSFGNLIEHLPEYTETFVNYMTTHENKNSYQFCYDRLPRDQFHARGGRYDQGALTSHSVMDALIRLQVLPPAPGQFNPGVNDIIDRNHTAYVDKIQQAAAAYLERAQNVFLMEDQTLLRLTIDTITALLLLRRLLWNGNVYGDKLKNNFQLGLIVSEATGTPTNNVILRGATGFDGKFKSGNNNFQFLCERYIAPLYTLNRTTELTEMFPGLVALCLDAHTQLSRGSLGRTVIDISSGQYQDRLISLIALELEHRRQNVTSLPIAAVVSIHDSVMLQYERGLGMLMHQPRVRAALEESRRLAQFNVNSDYDLLYFVCLGVIPQFASTP

Entity 7 polymer

描述 description	Large tegument protein deneddylase
分子量 formula_weight	306666.9 kDa
EC 编号 ec_number	3.4.19.12,3.4.22.-
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

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

MDIIPPIAVTVAGVGSRNQFDGALGPASGLSCLRTSLSFLHMTYAHGINATLSSDMIDGCLQEGAAWTTDLSNMGRGVPDMCALVDLPNRISYIKLGDTTSTCCVLSRIYGDSHFFTVPDEGFMCTQIPARAFFDDVWMGREESYTIITVDSTGMAIYRQGNISFIFDPHGHGTIGQAVVVRVNTTDVYSYIASEYTHRPDNVESQWAAALVFFVTANDGPVSEEALSSAVTLIYGSCDTYFTDEQYCEKLVTAQHPLLLSPPNSTTIVLNKSSIVPLHQNVGESVSLEATLHSTLTNTVALDPRCSYSEVDPWHAVLETTSTGSGVLDCRRRRRPSWTPPSSEENLACIDDGLVNNTHSTDNLHKPAKKVLKFKPTVDVPDKTQVAHVLPRLREVANTPDVVLNVSNVDTPESSPTFSRNMNVGSSLKDRKPFLFEQSGDVNMVVEKLLQHGHEISNGYVQNAVGTLDTVITGHTNVPIWVTRPLVMPDEKDPLELFINLTILRLTGFVVENGTRTHHGATSVVSDFIGPLGEILTGFPSAAELIRVTSLILTNMPGAEYAIKTVLRKKCTIGMLIIAKFGLVAMRVQDTTGALHAELDVLEADLGGSSPIDLYSRLSTGLISILNSPIISHPGLFAELIPTRTGSLSERIRLLCELVSARETRYMREHTALVSSVKALENALRSTRNKIDAIQIPEVPQEPPEETDIPPEELIRRVYEIRSEVTMLLTSAVTEYFTRGVLYSTRALIAEQSPRRFRVATASTAPIQRLLDSLPEFDAKLTAIISSLSIHPPPETIQNLPVVSLLKELIKEGEDLNTDTALVSWLSVVGEAQTAGYLSRREFDELSRTIKTINTRATQRASAEAELSCFNTLSAAVDQAVKDYETYNNGEVKYPEITRDDLLATIVRATDDLVRQIKILSDPMIQSGLQPSIKRRLETRLKEVQTYANEARTTQDTIKSRKQAAYNKLGGLLRPVTGFVGLRAAVDLLPELASELDVQGALVNLRTKVLEAPVEIRSQLTGDFWALFNQYRDILEHPGNARTSVLGGLGACFTAIIEIVPIPTEYRPSLLAFFGDVADVLASDIATVSTNPESESAINAVVATLSKATLVSSTVPALSFVLSLYKKYQALQQEITNTHKLTELQKQLGDDFSTLAVSSGHLKFISSSNVDDYEINDAILSIQTNVHALMDTVKLVEVELQKLPPHCIAGTSTLSRVVKDLHKLVTMAHEKKEQAKVLITDCERAHKQQTTRVLYERWTRDIIACLEAMETRHVFNGTELARLRDMAAAGGFDIHAVYPQARQVVAACETTAVTALDTVFRHNPHTPENTNIPPPLALLRGLTWFDDFSITAPVFTVMFPGVSIEGLLLLMRIRAVVLLSADTSINGIPNYRDMILRTSGDLLQIPALAGYVDFYTRSYDQFITESVTLSELRADIRQAAGAKLTEANKALEEVTHVRAHETAKLALKEGVFITLPSEGLLIRAIEYFTTFDHKRFIGTAYERVLQTMVDRDLKEANAELAQFRMVCQATKNRAIQILQNIVDTANATEQQEDVDFTNLKTLLKLTPPPKTIALAIDRSTSVQDIVTQFALLLGRLEEETGTLDIQAVDWMYQARNIIDSHPLSVRIDGTGPLHTYKDRVDKLYALRTKLDLLRRRIETGEVTWDDAWTTFKRETGDMLASGDTYATSVDSIKALQASASVVDMLCSEPEFFLLPVETKNRLQKKQQERKTALDVVLQKQRQFEETASRLRALIERIPTESDHDVLRMLLHDFDQFTHLPIWIKTQYMTFRNLLMVRLGLYASYAEIFPPASPNGVFAPIPAMSGVCLEDQSRCIRARVAAFMGEASVVQTFREARSSIDALFGKNLTFYLDTDGVPLRYRVCYKSVGVKLGTMLCSQGGLSLRPALPDEGIVEETTLSALRVANEVNELRIEYESAIKSGFSAFSTFVRHRHAEWGKTNARRAIAEIYAGLITTTLTRQYGVHWDKLIYSFEKHHLTSVMGNGLTKPIQRRGDVRVLELTLSDIVTILVATTPVHLLNFARLDLIKQHEYMARTLRPVIEAAFRGRLLVRSLDGDPKGNARAFFNAAPSKHKLPLALGSNQDPTGGRIFAFRMADWKLVKMPQKITDPFAPWQLSPPPGVKANVDAVTRIMATDRLATITVLGRMCLPPISLVSMWNTLQPEEFAYRTQDDVDIIVDARLDLSSTLNARFDTAPSNTTLEWNTDRKVITDAYIQTGATTVFTVTGAAPTHVSNVTAFDIATTAILFGAPLVIAMELTSVFSQNSGLTLGLKLFDSRHMATDSGISSAVSPDIVSWGLRLLHMDPHPIENACLIVQLEKLSALIANKPLTNNPPCLLLLDEHMNPSYVLWERKDSIPAPDYVVFWGPESLIDLPYIDSDEDSFPSCPDDPFYSQIIAGYAPQGPPNLDTTDFYPTEPLFKSPVQVVRSSKCKKMPVQPVQPAQPVQPAQPAQPVQPAQPIEPGTQIVVQNFKKPQSVKTTLSQKDIPLYVETESETAVLIPKQLTTSIKTTVCKSITPPNNQLSDWKNNPQQNQTLNQAFNKPILEITSIPTDDSISYRTWIEKSNQTQKRHQNDPRMYNSKTVFHPVNNQLPSWVDTAADAPQTDLLTNYKTRQPSPNFPRDVHTWGVSSNPFNSPNRDLYESDFSEPSDGYSSESENSIVLSLDEHRSCRVPRHVRVVNADVVTGRRYVRGTALGALALLSQACRRMIDNVRYTRKLLMDHTEDIFQGLGYVKLLLDGTYI

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7. 引用文献 (2)

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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	8.30 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	3804

fit	/app/data/saxs_computation/no/9no1/9no1.fit
pddf	/app/data/pr_computation/no/9no1/9no1.pr.out
profile	/app/data/saxs_computation/no/9no1/9no1.dat

Cryo-ET map of the VZV capsid vertex (5-fold axis).

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 (7)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

Entity 3 polymer

聚合体 Polymer

Entity 4 polymer

聚合体 Polymer

Entity 5 polymer

聚合体 Polymer

Entity 6 polymer

聚合体 Polymer

Entity 7 polymer

聚合体 Polymer

7. 引用文献 (2)

8. 文件与曲线 (10)

Files (7)

Curves (3)