9eug

;Cryo-EM structure of Staphylococcus aureus bacteriophage phi812 baseplate in the pre-contraction state - core, wedge module, and proximal tail proteins ;

Method: ELECTRON MICROSCOPY D_max: 222.4 Å Quality: REASONABLE

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	9eug
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 pre-contraction state - core, wedge module, and proximal tail 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	82.31 Å
回转半径 Rg (电子) rg_electron	82.83 Å
零角强度 I(0) i0	10873500000.00
分子量 molecular_weight	886880.0 kDa
排除体积 excluded_volume	1110200 Å³
包络体积 envelope_volume	2011800 Å³
水化壳体积 shell_volume	203940 Å³
包络直径 envelope_diameter	309.5 Å
壳层 Rg shell_rg	78.66 Å
包络 Rg envelope_rg	82.03 Å
形状 Rg shape_rg	82.82 Å
总 Rg total_rg	82.80 Å
总原子数 total_atoms	62523
残基数 n_residues	7900
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	222.4 Å
Rg (实空间) rg_real	78.48 Å
Rg 误差 (实空间) rg_real_error	0.77 Å
I(0) (实空间) i0_real	1.0450e+10
I(0) 误差 (实空间) i0_real_error	1.9720e+08
Rg (倒空间) rg_reciprocal	80.71 Å
I(0) (倒空间) i0_reciprocal	10820000000.0000
解质量估计 total_estimate	0.6868
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	81.9 Å
偏度 Skewness skewness	0.344
峰度 Kurtosis kurtosis	-0.566
角度范围 angular_range	— – 0.0950 Å⁻¹
当前正则化参数 α current_alpha	0.4851
最高正则化参数 α highest_alpha	1648000000.0000
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: 0.989; Stabil: 0.987; Sysdev: 0.008; Positv: 1.000; Valcen: 0.986; Smooth: 0.006

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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 (10)

Entity 1 polymer

描述 description	NlpC/P60 domain-containing protein
分子量 formula_weight	34645.9 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	A
原子数 atom_count	62523

MATDKEAKDVIDKFIDNVFNFDVLTKERIKEKDEEIKKITTDDMYEKVVYIRPYVGVIQSLNPQHVQYESFSNNGYDIEAELSFRKVSYLVDKGSIPTDSLSTLTVHLVERNQELLIDYFDEIQDVLYGEYMEEEYVFDEDVPLSTILALDLNDNLKSLSNIKYMFKGAPKENPFGTDKDVYIDTYNLLYWLYLGEDEELAYPMNINYFFTEGRFFTIFGKGHKYKVDVSKFIVGDILFFGRSDTNIGIYVGDGEFISMMGKFPKDETPIGKYKLDDYWNEFNGRVMRFDEEVYI

Entity 2 polymer

描述 description	GP-PDE domain-containing protein
分子量 formula_weight	96199.5 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	B

MVVRFQSSMGRSLKRVDSDDLNVKGLVLATVSKINYKYQSVEVKVNNLTLGSRIGDDGSLAVPYPKSFIGRTPEGSVFGTKPLITEGSVVLIGFLNDDINSPIILSVYGDNEQNKMINTNPLDGGKFDTESVYKYSSSLYEILPSLNYKYDDGEGTSIRTYNGKSFFSMTSGEEEKPQATDFYTGTEYQDLFTSYYGNKTLIEPRIQKAPNMLFKHQGVFYDDGTPDNHITTLFISERGDIRASVLNTETQKRTTQEMSSDGSYRVIKQDDDLMLDEAQVWIEYGISEDNKFYIKNDKHKFEFTDEGIYIDDKPMLENLDESIAEAMKNLNEIQKELDDINYLLKGVGKDNLEELIESTKESIEASKKATSDVNRLTTQIAEVSGRTEGIITQFQKFRDETFKDFYEDASTVINEVNQNFPTMKTDVKTLKTKVDNLEKTEIPNIKTRLTELENNNNNADKIISDRGEHIGAMIQLEENVTVPMRKYMPIPWSKVTYNNAEFWDSNNPTRLVVPKGITKVRVAGNVLWDSNATGQRMLRILKNGTYSIGLPYTRDVAISTAPQNGTSGVIPVKEGDYFEFEAFQDSEGDRQFRADPYTWFSIEAIELETETMEKDFMLIGHRGATGYTDEHTIKGYQMALDKGADYIELDLQLTKDNKLLCMHDSTIDRTTTGTGKVGDMTLSYIQTNFTSLNGEPIPSLDDVLNHFGTKVKYYIETKRPFDANMDRELLTQLKAKGLIGIGSERFQVIIQSFARESLINIHNQFSNIPLAYLTSTFSESEMDDCLSYGFYAIAPKYTTITKELVDLAHSKGLKVHAWTVNTKEEMQSLIQMGVDGFFTNYLDEYKKI

Entity 3 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	4

聚合体 Polymer

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

MKTRKLTNILSKLIDKTMAGTSKITDFTPGSASRSLLEAVSLEIEQFYILTKENIDWGIQEGIIEAFDFQKRQSKRAYGDVTIQFYQPLDMRMYIPAGTTFTSTRQEYPQQFETLVDYYAEPDSTEIVVEVYCKETGVAGNVPEGTINTIASGSSLIRSVNNEYSFNTGTKEESQEDFKRRFHSFVESRGRATNKSVRYGALQIPDVEGVYVYEETGHITVFAHDRNGNLSDTLKEDIIDALQDYRPSGIMLDVTGVEKEEVNVSATVTISNKSRIGDTLQKHIESVIRSYLNNLKTSDDLIITDLIQAIMNIDDVLIYDVSFDNLDENIIVPPQGIIRAGEIKVELK

Entity 4 polymer

描述 description	Peptidase C51 domain-containing protein
分子量 formula_weight	91364.3 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	E

MRRIRRPKVRIEIVTDDNTFTLRFEDTRDYNGDEFGAKLLGFQTKNSMEDDSSVFQINMAGDTYWDKLVMANDIIRIFITPNDDPNDKEGKQERLIQVGMVSQVSKVGSYGNDQTQFRITGQSFVKPFMKFGLGVIQEVQAVLPEVGWLIDGDGDNEVKFTGSSAHEVMTGIIRRFIPYMKYNYTEKTYNTIDNYLDYDDLSSWDEFEKLTEVSAFTNFDGSLKQLMDMVTARPFNELFFKNSEKTPGKAQLVLRKTPFNPTEWRALDMIKVPTEDFIEEDVGKSDVETYSIFTATPAGMLKELNGDVFSKPQFHPELTDRYGYTKFEVENIYLSTKSGSATEDSDSSGDDNGTERGTYSKIMKDLSNYGRDNISKGIDKYTSKLSSKYKNLKKAQAKKIIEKFVKEGKVTEKEYEKITGNKVDDELTSDNRPKLTKDKLKSILKEKFKTQDDFNNSKKKKKAKTDALKELTTKYRFGNKTHATTLLDEYIKYKGEPPNDEAFDKYLKAIEGVSNVATDTGSDASDSPLVMFSRMLFNWYHGNPNFYAGDIIVLGDPKYDLGKRLFIEDKQRGDTWEFYIESVEHKFDYKQGYYTTVGVTRGLKDAILEDGKGSPHRFAGLWNQSSDFMGGLMGEDTSKELKEKGVAEKQSSGDKDGGSDSGGAQDGGSLDSLKKYNGKLPKHDPSFVQPGNRHYKYQCTWYAYNRRGQLGIPVPLWGDAADWIGGAKGAGYGVGRTPKQGACVIWQRGVQGGSPQYGHVAFVEKVLDGGKKIFISEHNYATPNGYGTRTIDMSSAIGKNAQFIYDKK

Entity 5 polymer

描述 description	Baseplate component
分子量 formula_weight	19998.7 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	F,G

MNNFIPQPQGLLRFLNTLDTDLTSSHMNLLDEEVSFVSKFYTPQLQLSELAKKVLTNIKTDDIPVLEREFNDNTIIHKANDTLLKVQAPRMYMILQSIVLEAYAIVNCFVENPSSLKYLTEEDVSITRENLNYVADYLGNYDDYNSVVLDLRDLDLCFSAIELQLPLIKKEANV

Entity 6 polymer

描述 description	TmpF
分子量 formula_weight	116389.9 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	H,J

MANFLKNLHPLLRRDRNKKDNQDPNFALIDALNEEMNQVEKDAIESKLQSSLKTSTSEYLDKFGDWFGVYRKTDEKDDVYRARIIKYLLLKRGTNNAIIDAIKDYLGRDDIDVSVYEPFTNIFYTNKSHLNGEDHLMGYYYRFAVINVSIGDYFPVEIIDVINEFKPAGVTLYVTYDGASTIRGGAIIKWLDGLPKIETYQEFDRFTGYDDTFYGHINMNQSKDTDNSSSDIFKTNHSLINSLDVLTGSSSVGRQYINYGYVTSYVYNPGMTSSVNQISASTEGRGQEVPTDYYMYTSTKNNNTVELSMQTTSGVSYLYNNFNFRDYMSKYRPQVDLQSDEARRIVSDYIKELSIDYYLSAVIPPDESIEIKLQVYDFSINRWLTVSINNLSFYEKNIGSNIGYIKDYLNSELNMFTRLEINAGKRDSVDIKVNYLDLMFYYYERGIYTIKPYKALIENYLDISRETYVEAFKIASLSNGDIITKTGFQPIGYLKLVGNYENTIPSTINIVAKDTDNNPIESNELDVYNTVENRNLLQSYKGVNTIAREITSTKEFTVSGWAKEIYSTNYLSKVLKPGKVYTLSFDMEITGNDPTLKSYSDNHGIYLYSNTKGIVVNGVKSMERTIGNKVSVTQTFTAPTITDHRLLIYTGRYTSDGKASTPPVFFNTVKITELKLTEGSSKLEYSPAPEDKPNVIEKGIKFNNILTNIQTLSINSDTILKNVTLYYSYYGDSWVELKTLGNISTGETTETNNLIDLYGLQTVDYSNINPMSKVSLRSIWNVKLGELNNQEGSLSNMPNDYFNAVWQDIDKLSDIELGSMRMVKDTEGGVFDGATGEIIKATLFNVGAYTDLDMLAYTLTNYTEPLTLGSSRLISELKEELLTSESFNVDNRIKVIDSIYEELPNTSIIKNGFVEREVTGSKYLDYGLYEPIEDGTRYKLIVEGEFKDNIEFISLYNSNPNFNETFIYPSEIINGVAEKEFIAKPSTEDKPRLNTDVRIYIRPYDSTISKVRRVELRKV

Entity 7 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	2

聚合体 Polymer

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

MRFKKHVVQHEETMQAIAQRYYGDVSYWIDLVEHNNLKYPYLVETDEEKMKDPERLASTGDTLIIPIESDLTDVSAKEINSRDKDVLVELALGRDLNITADEKYFNEHGTSDNILAFSTNGNGDLDTVKGIDNMKQQLQARLLTPRGSLMLHPNYGSDLHNLFGLNIPEQATLIEMEVLRTLTSDNRVKSANLIDWKIQGNVYSGQFSVEIKSVEESINFVLGQDEEGIFALFE

Entity 8 polymer

描述 description	Putative baseplate component
分子量 formula_weight	29381.6 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	M,N

MPQSDGISNLHRIALRFPKEGGGYDMYRFKVNPENYTIDSPQRTTAIKTKSDIVIEDYGKDIEVINFTGTTGFRPVREADGLKTGKQKMEELQSRVSEYAMQGGSGNVSGSYLQFFNFTDDSYYKVHLAPQGLKITRSKDEPLLFRYEITLVVIGSLTEADRSAVTTEEFGNVKPNASQRVDEGIKELDKNARKTRDRNNQEISRRENTIPKSTGDNTNEGNRLKQSFPSSSIYNPRQSTNGLKGNIDNMALIIGYGDGGVSS

Entity 9 polymer

描述 description	Major tail sheath protein
分子量 formula_weight	64559.0 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	P,Q,T,U,X,Y

MAVEPFPRRPITRPHASIEVDTSGIGGSAGSSEKVFCLIGQAEGGEPNTVYELRNYSQAKRLFRSGELLDAIELAWGSNPNYTAGRILAMRIEDAKPASAEIGGLKITSKIYGNVANNIQVGLEKNTLSDSLRLRVIFQDDRFNEVYDNIGNIFTIKYKGEEANATFSVEHDEETQKASRLVLKVGDQEVKSYDLTGGAYDYTNAIITDINQLPDFEAKLSPFGDKNLESSKLDKIENANIKDKAVYVKAVFGDLEKQTAYNGIVSFEQLNAEGEVPSNVEVEAGEESATVTATSPIKTIEPFELTKLKGGTNGEPPATWADKLDKFAHEGGYYIVPLSSKQSVHAEVASFVKERSDAGEPMRAIVGGGFNESKEQLFGRQASLSNPRVSLVANSGTFVMDDGRKNHVPAYMVAVALGGLASGLEIGESITFKPLRVSSLDQIYESIDLDELNENGIISIEFVRNRTNTFFRIVDDVTTFNDKSDPVKAEMAVGEANDFLVSELKVQLEDQFIGTRTINTSASIIKDFIQSYLGRKKRDNEIQDFPAEDVQVIVEGNEARISMTVYPIRSFKKISVSLVYKQQTLQA

Entity 10 polymer

描述 description	Capsid protein
分子量 formula_weight	15943.0 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	R,S,V,W,Z,a

MASEAKQTVHTGNTVLLMIKGKPVGRAQSASGQREYGTTGVYEIGSIMPQEHVYLRYEGTITVERLRMKKENFADLGYASLGEEILKKDIIDILVVDNLTKQVIISYHGCSANNYNETWQTNEIVTEEIEFSYLTASDKART

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7. 引用文献 (1)

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分辨率 resolution	4.50 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	9705

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

;Cryo-EM structure of Staphylococcus aureus bacteriophage phi812 baseplate in the pre-contraction state - core, wedge module, and proximal tail 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 (10)

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

Entity 9 polymer

聚合体 Polymer

Entity 10 polymer

聚合体 Polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)