9euk

;Cryo-EM structure of Staphylococcus aureus bacteriophage phi812 baseplate in the post-contraction state - sheath initiator, wedge module, and inner tripod proteins ;

Method: ELECTRON MICROSCOPY D_max: 231.6 Å Quality: GOOD

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	9euk
沉积日期 deposition_date	2024-03-27
结构标题 title	;Cryo-EM structure of Staphylococcus aureus bacteriophage phi812 baseplate in the post-contraction state - sheath initiator, wedge module, and inner tripod proteins ;
关键词 keywords	bacteriophage, phage, contractile, phi812, 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	80.80 Å
回转半径 Rg (电子) rg_electron	82.12 Å
零角强度 I(0) i0	2518300000.00
分子量 molecular_weight	421790.0 kDa
排除体积 excluded_volume	526660 Å³
包络体积 envelope_volume	959700 Å³
水化壳体积 shell_volume	105520 Å³
包络直径 envelope_diameter	287.9 Å
壳层 Rg shell_rg	65.81 Å
包络 Rg envelope_rg	82.75 Å
形状 Rg shape_rg	82.11 Å
总 Rg total_rg	81.90 Å
总原子数 total_atoms	29739
残基数 n_residues	3756
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	231.6 Å
Rg (实空间) rg_real	78.03 Å
Rg 误差 (实空间) rg_real_error	1.37 Å
I(0) (实空间) i0_real	2.4620e+09
I(0) 误差 (实空间) i0_real_error	4.7780e+07
Rg (倒空间) rg_reciprocal	76.63 Å
I(0) (倒空间) i0_reciprocal	2490000000.0000
解质量估计 total_estimate	0.8563
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	60.9 Å
偏度 Skewness skewness	0.533
峰度 Kurtosis kurtosis	-0.547
角度范围 angular_range	— – 0.0950 Å⁻¹
当前正则化参数 α current_alpha	0.1464
最高正则化参数 α highest_alpha	135100000.0000
实空间数据点数 n_real_points	20
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.816; Stabil: 0.974; Sysdev: 1.000; Positv: 1.000; Valcen: 0.960; Smooth: 0.271

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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 (4)

Entity 1 polymer

描述 description	Baseplate wedge subunit
分子量 formula_weight	26611.8 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	A
原子数 atom_count	29739

MRFKKHVVQHEETMQAIAQRYYGDVSYWIDLVEHNNLKYPYLVETDEEKMKDPERLASTGDTLIIPIESDLTDVSAKEINSRDKDVLVELALGRDLNITADEKYFNEHGTSDNILAFSTNGNGDLDTVKGIDNMKQQLQARLLTPRGSLMLHPNYGSDLHNLFGLNIPEQATLIEMEVLRTLTSDNRVKSANLIDWKIQGNVYSGQFSVEIKSVEESINFVLGQDEEGIFALFE

Entity 2 polymer

描述 description	Baseplate component
分子量 formula_weight	39248.9 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	B,C

MKTRKLTNILSKLIDKTMAGTSKITDFTPGSASRSLLEAVSLEIEQFYILTKENIDWGIQEGIIEAFDFQKRQSKRAYGDVTIQFYQPLDMRMYIPAGTTFTSTRQEYPQQFETLVDYYAEPDSTEIVVEVYCKETGVAGNVPEGTINTIASGSSLIRSVNNEYSFNTGTKEESQEDFKRRFHSFVESRGRATNKSVRYGALQIPDVEGVYVYEETGHITVFAHDRNGNLSDTLKEDIIDALQDYRPSGIMLDVTGVEKEEVNVSATVTISNKSRIGDTLQKHIESVIRSYLNNLKTSDDLIITDLIQAIMNIDDVLIYDVSFDNLDENIIVPPQGIIRAGEIKVELK

Entity 3 polymer

描述 description	TmpF
分子量 formula_weight	116391.9 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	D

MANFLKNLHPLLRRDRNKKDNQDPNFALIDALNEEMNQVEKDAIESKLQSSLKTSTSEYLDKFGDWFGVYRKTDEKDDVYRARIIKYLLLKRGTNNAIIDAIKDYLGRDDIDVSVYEPFTNIFYTNKSHLNGEDHLMGYYYRFAVINVSIGDYFPVEIIDVINEFKPAGVTLYVTYDGASTIRGGAIIKWDDGLPKIETYQEFDRFTGYDDTFYGHINMNQSKDTDNSSSDIFKTNHSLINSLDVLTGSSSVGRQYINYGYVTSYVYNPGMTSSVNQISASTEGRGQEVPTDYYMYTSTKNNNTVELSMQTTSGVSYLYNNFNFRDYMSKYRPQVDLQSDEARRIVSDYIKELSIDYYLSAVIPPDESIEIKLQVYDFSINRWLTVSINNLSFYEKNIGSNIGYIKDYLNSELNMFTRLEINAGKRDSVDIKVNYLDLMFYYYERGIYTIKPYKALIENYLDISRETYVEAFKIASLSNGDIITKTGFQPIGYLKLVGNYENTIPSTINIVAKDTDNNPIESNELDVYNTVENRNLLQSYKGVNTIAREITSTKEFTVSGWAKEIYSTNYLSKVLKPGKVYTLSFDMEITGNDPTLKSYSDNHGIYLYSNTKGIVVNGVKSMERTIGNKVSVTQTFTAPTITDHRLLIYTGRYTSDGKASTPPVFFNTVKITELKLTEGSSKLEYSPAPEDKPNVIEKGIKFNNILTNIQTLSINSDTILKNVTLYYSYYGDSWVELKTLGNISTGETTETNNLIDLYGLQTVDYSNINPMSKVSLRSIWNVKLGELNNQEGSLSNMPNDYFNAVWQDIDKLSDIELGSMRMVKDTEGGVFDGATGEIIKATLFNVGAYTDLDMLAYTLTNYTEPLTLGSSRLISELKEELLTSESFNVDNRIKVIDSIYEELPNTSIIKNGFVEREVTGSKYLDYGLYEPIEDGTRYKLIVEGEFKDNIEFISLYNSNPNFNETFIYPSEIINGVAEKEFIAKPSTEDKPRLNTDVRIYIRPYDSTISKVRRVELRKV

Entity 4 polymer

描述 description	DUF4815 domain-containing protein
分子量 formula_weight	129263.0 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	E,F,G

MAINFKGSPYLDRFDPSKDRTKVLFNPDRPLQQAELNEMQSIDQYYLKNLGDAIFKDGDKQSGLGFTLSEDNVLTVNPGYVYINGKIRYYDNDDSVKITGVGKETIGIKLTERIVTPDEDASLLDQTSGVPSYFSKGADRLEEKMSLTVNDPTSATIYTFMDGDLYIQSTNAEMDKINKVLAERTYDESGSYKVNGFELFSEGNAEDDDHVSVVVDAGKAYVKGFKVDKPVSTRISVPKSYDLGTAENESTIFNKSNNSISLANSPVKEIRRVTGQVLIEKERVTRGAQGDGQDFLSNNTAFEIVKVWTETSPGVTTKEYKQGEDFRLTDGQTIDWSPQGQEPSGGTSYYVSYKYNKRMEAGKDYEVTTQGEGLSKKWYINFTPSNGAKPIDQTVVLVDYTYYLARKDSVFINKYGDIAILPGEPNIMRLVTPPLNTDPENLQLGTVTVLPDSDEAVCISFAITRLSMEDLQKVKTRVDNLEYNQAVNALDDGAMEGQNPLTLRSVFSEGFISLDKADITHPDFGIVFSFEDAEATLAYTEAVNQPKIIPGDTTAHIWGRLISAPFTEERTIYQGQASETLNVNPYNIPNKQGVLKLTPSEDNWIDTENVTITEQKTKKVTMKRFWRHNESYYGETEHYLYSNLQLDAGQKWKGETYAYDREHGRTGTLLESGGQRTLEEMIEFIRIRDVSFEVKGLNPNDNNLYLLFDGVRCAITPATGYRKGSEDGTIMTDAKGTAKGKFTIPAGIRCGNREVTLKNANSTSATTYTAQGRKKTAQDIIIRTRVTVNLVDPLAQSFQYDENRTISSLGLYFASKGDKQSNVVIQIRGMGDQGYPNKTIYAETVMNADDIKVSNNASAETRVYFDDPMMAEGGKEYAIVIITENSDYTMWVGTRTKPKIDKPNEVISGNPYLQGVLFSSSNASTWTPHQNSDLKFGIYTSKFNETATIEFEPIKDVSADRIVLMSTYLTPERTGCTWEMKLILDDMASSTTFDQLKWEPIGNYQDLDVLGLARQVKLRATFESNRYISPLMSSSDLTFTTFLTELTGSYVGRAIDMTEAPYNTVRFSYEAFLPKGTKVVPKYSADDGKTWKTFTKSPTTTRANNEFTRYVIDEKVKSSGTNTKLQVRLDLSTENSFLRPRVRRLMVTTRDE

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7. 引用文献 (1)

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分辨率 resolution	3.10 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	25203

fit	/app/data/saxs_computation/eu/9euk/9euk.fit
pddf	/app/data/pr_computation/eu/9euk/9euk.pr.out
profile	/app/data/saxs_computation/eu/9euk/9euk.dat

;Cryo-EM structure of Staphylococcus aureus bacteriophage phi812 baseplate in the post-contraction state - sheath initiator, wedge module, and inner tripod proteins ;

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 (4)

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

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)