8rk3

Bacteriophage JBD30 baseplate - composite structure

Method: ELECTRON MICROSCOPY D_max: 322.5 Å Quality: EXCELLENT

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	8rk3
沉积日期 deposition_date	2023-12-23
结构标题 title	Bacteriophage JBD30 baseplate - composite structure
关键词 keywords	bacteriophage JBD30, virion, baseplate, 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	— Å
回转半径 Rg (电子) rg_electron	126.60 Å
零角强度 I(0) i0	37733900000.00
分子量 molecular_weight	1645400.0 kDa
排除体积 excluded_volume	2050600 Å³
包络体积 envelope_volume	3929800 Å³
水化壳体积 shell_volume	277630 Å³
包络直径 envelope_diameter	375.3 Å
壳层 Rg shell_rg	88.04 Å
包络 Rg envelope_rg	125.20 Å
形状 Rg shape_rg	126.70 Å
总 Rg total_rg	126.30 Å
总原子数 total_atoms	116259
残基数 n_residues	15222
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	322.5 Å
Rg (实空间) rg_real	122.20 Å
Rg 误差 (实空间) rg_real_error	1.15 Å
I(0) (实空间) i0_real	3.6130e+10
I(0) 误差 (实空间) i0_real_error	8.1410e+08
Rg (倒空间) rg_reciprocal	121.70 Å
I(0) (倒空间) i0_reciprocal	36890000000.0000
解质量估计 total_estimate	0.9086
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	161.2 Å
偏度 Skewness skewness	0.066
峰度 Kurtosis kurtosis	-0.765
角度范围 angular_range	— – 0.0600 Å⁻¹
当前正则化参数 α current_alpha	1.0370
最高正则化参数 α highest_alpha	668700000.0000
实空间数据点数 n_real_points	13
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.999; Stabil: 0.942; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; 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 (8)

Entity 1 polymer

描述 description	Tape measure protein N-terminal domain-containing protein
分子量 formula_weight	120920.6 kDa
来源方法 src_method	nat
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C
原子数 atom_count	116259

MATNQQLSIALRIQADLAEAQNALRQLTGNLQQVDRGAVQTRSELSAMGGQLDSLRAQVLGFVGAWASLSALGGLVTMVDQYGQMADRIQMVTSSTAEYEQVQARLLETASRTYRPLAEAQELYIRTADSLKSLRYTTEQALDITDSFSFLLVTNAASADRAASAIDAYSKSIQTGKVSSDAWQSIMAAMPSLVNALAESTGKSTEEIRKLGIEGSLSLRDLNEGLRKTVAANREAADNMGTSVQDALVSLNNALSAYLGELNRTYDITGSVSSALNVLAENMEVIVKLFGVAAVAGLTRYVASLTLATQAKLAAVLAARAQAAEELRTAQAQVASTAAAAANARAQAGLTVSHTQAAAAEAAHTAATQRLAAAQLAAGAAMRGMLAVIGGPAGIAMLVAGAAASFFLFRDSAQAVKSSLDDLSEPLDQVVERMGKLSEIEQDRELTRLSEQIDGLRQTAVEAAREMREVASTALYGARLDRIPSAEAQQALQPLIDASADAARGVEVDWKSVMDTLAASGAVPDSLKRKLLDMAAGQAEAGRTATELGQRHAELKARLEGSTAAINENSDALSKGSDKAAEYIQSLRLAIADLEDPSVLGKAGRRLQQFGADLNAEQSAEILRLETLKANTEKAAQAREDARRKAESSARQQASTAEQLAKSQEGYVAGLEKQARTLGLTSAEVRAYELAEKGLTGALHARAAAALAALAADEKKRQADANARTNAGLEAEYLRATGRTVDAGLLEIRTKFDAMRRDFEKAGNDAGLAWIDKLIPVAEAKVRLDDVKQQMDDLLADQQRAESSVNVQQDAGVINEMDARQRILDIHRATYEKLQQIRPILEQMARQPGEVGRAAAESLAQLDAEAARLQQTTTLLETTLRDGLTTGFTDAIKGLASGTMDLRDAITSLGEAVLNALVNMAAQNLAQSLSSGIMGLFGGGQQDTSMTTGAAAVTASAGALSTAGASLLTGAAAIQAAAASLAAANGVQGLGAAAGGAGAAGAAAGGGSWLSSIAGIFGFASGGHIKGPGTGTSDSIPILASNDEFMTRAAVVRQPGALAFLEQFNRYGMAALAGWANPVRHATGGQIGTPAPNLPAPVRAGANLPEPSKNFSTSVANSIYLHAVQDTDQMAADMWAGKGGEHFLVWLNKNRQAVKQII

Entity 2 polymer

描述 description	DUF2163 domain-containing protein
分子量 formula_weight	29979.1 kDa
来源方法 src_method	nat
拷贝数 entity_count	3

聚合体 Polymer

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

MSFNSRESSLADGQPVRLYQFSRGAIRWSYNSSDRDITYQNQIFRTVPGGITDNGIICSGDPQSDQFVITAPADLDVALLYKTRSPSDAIDLVVYDMHYGDAEAAVSWVGQIGDVDWPTVDSCRITCVSEDELMDQPGLTDTYCRTCTAIVGDHRCKVNLVPYRVTLTPQSVSAWVISSGVVAGYADGWFTGGYVEWQVDGDNYDRRFIEQHAGADLHILGGTEGIPAGGQLRVYPGCDGLAQTCDDKFSNLPNFRGFNAMQGKSPFDGDQVW

Entity 3 polymer

描述 description	Virion structural protein
分子量 formula_weight	62163.1 kDa
来源方法 src_method	nat
拷贝数 entity_count	3

聚合体 Polymer

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

MATFPGFQVPKPVEGIVAGITPNIDALELNQDISLAAVAASTWGGAYGAHQPVEVIHSTYQAVHQSALEENYYNRLWLIPTAMELGNVVSTQIRPASVWNAYFSPRTLTAIDREAADGITLSGQASPPLGFAALEERTWTVSIGTDGPPVVNARIVWRLQGEPNLVLVITGNRIIAWTFAPDWGDSIVERLSASTNILQSESAVTQRRAMRLAPRREFDANMYAVDRERQLLDMTLFGWGARIWALPIWPDIQLLHQPLAAGSLGIPCDTAGLDFRDGGLAMLRGEDAFTYEVVEVKTVTASGLDLVRPVQAAWGTGSRLYPVRTAQLTEQPTLTRLTDTAQSARVSFLVMEPSAWPELMPATTYRGRPVLEQRPDESEDLTSSYQRLLSTLDNGSAIPRVTDVAGMALPVIGHRWIGMGRAERSAFRSLVYALRGQQKPLWVPTHADDLTLVATVSQLSTALDVRNIGYARFANGRPGRRDIRIELYDGTVYHRRILTSTELDADTERVAIDAALGRLVEPTDVARICFMALCSAASDVVEIEHVTDSEGVATAALTFKGVRDDEF

Entity 4 polymer

描述 description	DUF2793 domain-containing protein
分子量 formula_weight	40578.4 kDa
来源方法 src_method	nat
拷贝数 entity_count	9

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	a,W,e,I,E,M,J,F,N

MTLYMGPNTGLLINGLPGEGHYSDLIRMWRWDDFLRQPVVKGRVATLPTTGQAEGDTYIFTGSGSNQNRLARWWATGATTAIWEYMPPRLGWRVQVANETTPSGQVKTYEYSGTAWVELVGGMSDAPSDGKAYARESGAWTELGSAAKSALNVLPFMNLMPDMGRFAGTAANPLATMFTTSWTPSSFLNGWNGATVADGGKFAFDNSTNGGAGPALNARVQALLAAMGRTWTSVSRYGVEFFTAVLTAGSQTTTGSAGADGVTRYLCCSNGSKTVFNAGGWATVVMWLRVESGSAHISSAPYTTHRLWINGAVAAPGVVLPANQWVHLRFSMQSYNGYDNACPYIYASAGAQIAFACPAWFGGLVDPGIHVAPILTINGASA

Entity 5 polymer

描述 description	Tip attachment protein J domain-containing protein
分子量 formula_weight	79898.8 kDa
来源方法 src_method	nat
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	o,b,d

MGAKPKAQTVGWRYYFDIHFALGKKVDEVCAIRASGKTAWKGSITSNGQVRINAPELFGGDKGEGGLDGTLDVLFGEEDQGVLPRLAAMLGGLVPAFRGVTTCFYSGLVTSVNPYPKKWEILRRGGNRLWDGNPWYPEKQFVWLADGQIKAMNPAHILYLVYTGRDFRGLARTRMDEASWRAAADTLYAEGFGLCFEWTRSDSFKNFCETVKSHIGAEVYPNRQTGQISIRLLRDDYNVADLPLFDEDSGLLEITQEKTGSTSLAPSQLIVKYIDQIDGAQRQIIVNNNAVAASQGRRSSEEIEFLGVPTGELAGRVGEREMRLKTTGLKRYKGVFDRRARSLNPGQPFLIRSTPRGIPETVVRVGRIEDNFLGDGKITLTVVQDQFNLPATTGVAPPPPGWTPPDRTPRAITVRRLIEAPYRELAGVIDPANLQLLDVSASYLAALAEAPTSLSQSYTLTDRVGSSGAFVDRGTGDWCPTGLLAAELPLAAGPNVVTLTNATRLEDVTVGQAAVVDDEIVRVDAVNYASGTVTLARGCADTVPAKHLAGARVWFYDTFEAVDETVYSQGVTLQARLLTNTSEGQLAPALAATDSLTLTGRQGKPYPPGQFRINGSAYPTKVYGALSVSWAKRDRIGQADQLIDTTVGNIGPEDGATVTLQVYSGTTLKRTYAGLTSSSWSYPLAEDMADGPLQDVRLVLRSVRDGIDSWQQHDITIERHGLGFRLGEELGGVSA

Entity 6 polymer

描述 description	Virion structural protein
分子量 formula_weight	35014.1 kDa
来源方法 src_method	nat
拷贝数 entity_count	9

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	c,i,k,K,Q,T,L,R,V

MATEFGTAVNHADLVERLVQFLTASPDLVAAGQAYEKVFDNTIPASGTAIAVRQVTLRAPGLGGTDAIYMGIQSYGDTALDYYNLRLMGGTAFNPGAIPPGGDYWTAFANYSPRVQLLAWNQPMPYWFFANGRRFWIVVKVSTIYESAGAGFILPPCPPSQYPYPLAVVGSYRGDVATRWSDVSDRHRGISSPYERSCYLRDPAGRWLGFTVDGGAANESDYNNRTLLPLGCGRYAGSSDTVVKQLRDSFGKFPLKALQFVTRETEGRRYLGDFDGAFYVPTLNSGAEDVIVEDGVDHVVFQTAWRSGNPWLYAIRKD

Entity 7 polymer

描述 description	Virion structural protein
分子量 formula_weight	33358.8 kDa
来源方法 src_method	nat
拷贝数 entity_count	9

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	S,Y,m,n,G,X,p,H,Z

MAYFTGTANNPADLLAKVRVHAESLGWVTDRASASEWLCHNADGYWSFNAGANQFQMAGNTGFDNSLAWNAQPGNSVQNNPYSSKGPTVAQLSGGPFTRYHLFATAAYLHLHVEIAAGQFRPVMIGSLNKRGVGYTGGQYVCGSFIYTPGQALTNNWSSHPFDGYHIQYSNSSCMLRLDGLDGGPSPEWLPFDYTTNVPRRVVGPGRGNYSSQYHPDVGLIDASANELNSSTTTVPCAIYAFGAQQRSRYVGEVPDFGICNMAFLAPGDPLVVGSDTWRVYPLLQRGTATDFDSTSAWVGYCFRVVE

Entity 8 polymer

描述 description	Virion structural protein
分子量 formula_weight	26983.7 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	q,s,f,j,h,l

MAQETYFYGQGEIDAAPIVNGVLGKWRWIQDVSAMSIQLAVEKVEHKESYSGQKALVRSFPIGKTATVNITLHSIGPDNLALTLYGKVVAKAAGSVTGEVLPADLVAGDVIRLANFGVSELVITDSASSPAPLDPQYYALRADGAYGEVQLLGLPTPAPTQPFKAAYEYAATKQVGMFTAPQPTVALRYKGINLAEGGAPVIVELYKVATDPLQELALISDGNTVAGMQISGGILLDTSKPDTGDLGRFGRIIQLG

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7. 引用文献 (2)

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分辨率 resolution	4.46 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	1780

fit	/app/data/saxs_computation/rk/8rk3/8rk3.fit
pddf	/app/data/pr_computation/rk/8rk3/8rk3.pr.out
profile	/app/data/saxs_computation/rk/8rk3/8rk3.dat

Bacteriophage JBD30 baseplate - composite structure

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

冷冻电镜 EM 3D

5. 实体与聚合体信息 (8)

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

Entity 8 polymer

聚合体 Polymer

7. 引用文献 (2)

8. 文件与曲线 (10)

Files (7)

Curves (3)