9ki1

Baseplate structure of Escherichia phage Mu

Method: ELECTRON MICROSCOPY D_max: 274.0 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	9ki1
沉积日期 deposition_date	2024-11-11
结构标题 title	Baseplate structure of Escherichia phage Mu
关键词 keywords	phage, sheath, tube, 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	79.71 Å
回转半径 Rg (电子) rg_electron	79.28 Å
零角强度 I(0) i0	37230500000.00
分子量 molecular_weight	1625400.0 kDa
排除体积 excluded_volume	2025800 Å³
包络体积 envelope_volume	3282900 Å³
水化壳体积 shell_volume	318290 Å³
包络直径 envelope_diameter	250.2 Å
壳层 Rg shell_rg	93.30 Å
包络 Rg envelope_rg	77.38 Å
形状 Rg shape_rg	79.29 Å
总 Rg total_rg	79.35 Å
总原子数 total_atoms	114473
残基数 n_residues	15018
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	274.0 Å
Rg (实空间) rg_real	80.75 Å
Rg 误差 (实空间) rg_real_error	1.16 Å
I(0) (实空间) i0_real	3.6570e+10
I(0) 误差 (实空间) i0_real_error	6.6930e+08
Rg (倒空间) rg_reciprocal	81.19 Å
I(0) (倒空间) i0_reciprocal	37390000000.0000
解质量估计 total_estimate	0.9116
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	95.9 Å
偏度 Skewness skewness	0.277
峰度 Kurtosis kurtosis	-0.065
角度范围 angular_range	— – 0.1000 Å⁻¹
当前正则化参数 α current_alpha	1.3270
最高正则化参数 α highest_alpha	8703000000.0000
实空间数据点数 n_real_points	21
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.751; Stabil: 0.930; Sysdev: 1.000; Positv: 1.000; Valcen: 0.923; Smooth: 0.903

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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 (12)

Entity 1 polymer

描述 description	DNA circularization protein N
分子量 formula_weight	52086.0 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	0,s,t,u,v,w
原子数 atom_count	114473

MFEDALNAVNAVRDKTGGGRKTTGKGTFRNVPFLVIEEQKQAGGRRLVKREYPLRDTGGVNDLGKKLRSRTFSACILNSNAETARDEAGALMDALDAPGSGELVHPDFGTVDVMVDSWECRTKADELNYYAFTVTVYPSLQDTAPDAETDTSAAVPAQAVAVTGSLGDTLSSVWQTVKDGTAAATAVMEAVTGVIDDISDAVDNLGVTQTVSGLMGSLSAMKGSVTSLINQPAMLASSLMGALSGVSSLCDTRTAFSTWNRLAQRFERRHAATAGRQGTITTSYNSPVAEKNIATLNYVMLAAAQTYRAEAASQALTAALDFSRRMDNAARAPVLDAPSTTTGTASGASSTSATVTQGQLQLTAITPDGGFSQVSFSDSGTATPPVFESVSDIEKTTAMLGAALDSVILTASEQGFSTDSVQLTQLRLLVVADLEKRGLQLAGSESHHLPETLPAMVALYRFTGNSRNWQRLARRNGISNPLFVPGGVSIEVINE

Entity 2 polymer

描述 description	Tail sheath protein
分子量 formula_weight	53132.5 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	1,2,3,x,y,z

MSDISFNAIPSDVRVPLTYIEFDNSNAVSGTPAPRQRVLMFGQSGSKASAAPNVPVRIRSGSQASAAFGQGSMLALMADAFLNANRVAELWCIPQGNGTGNAAVGEISLSGTAGENGSLVTYIAGQRLAVSVAAGATGAALADLLVARIKGQPDLPVTAEVRADSGDDDTHADVVLSAKFTGALSAVDVRWNYYAGETTPYGIITAFKAASGKNGNPDISASIAGMGDLQYKYIVMPYTDEPNLNLLRTELQERWGPVNQADGFAVTVLSGTYGDISTFGVSRNDHLISCMGIAGAPEPSYLYAATLCAVASQALSIDPARPLQTLTLPGRMPPAVGDRFTWSERNALLFDGISTFNVNDGGEMQIERMITMYRTNKYGDSDPSYLNVNTIATLSYLRYSLRTRITQKFPNYKLASDGTRFATGQAVVTPSVIKTELLALFEEWENAGLVEDFDTFKEELYVARNKDDKDRLDVLCGPNLINQFRIFAAQVQFIL

Entity 3 polymer

描述 description	Tail tube protein
分子量 formula_weight	12840.5 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	4,5,6,7,8,9

MAGNQRQGVAFIRVNGMELESMEGASFTPSGITREEVTGSRVYGWKGKPRAAKVECKIPGGGPIGLDEIIDWENITVEFQADTGETWMLANAWQADEPKNDGGEISLVLMAKQSKRIA

Entity 4 polymer

描述 description	Baseplate protein gp46
分子量 formula_weight	16340.2 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	A,B,C,D,E,F

MTDLAIIWTNGRGDIAQDGIDMLTDDSLTTDVTISLFTDRRALDSDTLPDGSDDRRGWWGDSYRDRPIGSRLWLLSREKATPDTLERARGYAEEALEWLKTAGRVSAINVRAEQLHQGWLYLYIALTLPDGSVIPYEFKAAFNGV

Entity 5 polymer

描述 description	Baseplate hub protein gp44
分子量 formula_weight	41840.1 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,N,U

MSNTVTLRADGRLFTGWTSVSVTRSIESVAGYFELGVNVPPGTDLSGLAPGKKFTLEIGGQIVCTGYIDSRRRQMTADSMKITVAGRDKTADLIDCAAVYSGGQWKNRTLEQIARDLCAPYGVTVRWELSDKESSAAFPGFTLDHSETVYEALVRASRARGVLMTSNAAGELVFSRAASTATDELVLGENLLTLDFEEDFRDRFSEYTVKGYARANGAEGDDIDAKSIVSRKGTATDSDVTRYRPMIIIADSKITAKDAQARALREQRRRLAKSITFEAEIDGWTRKDGQLWMPNLLVTIDASKYAIKTTELLVSKVTLILNDQDGLKTRVSLAPREGFLVPVESDRKNRKGGDSNGGIDALVEDYYRRHPEKTPPWKE

Entity 6 polymer

描述 description	Baseplate protein gp47
分子量 formula_weight	38724.6 kDa
来源方法 src_method	nat
拷贝数 entity_count	12

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	H,I,J,K,L,M,O,P,Q,R,S,T

MAYSPPTLSSLIARTEQNIEQRLPGSWPQAREKTLSAIAYAQAGLAAGCHEHISWVGRQIIPSTADEDELLEHCRFWGVRRKQATAASGPLTVTTSAATTIPAGTRWQRADGVVYSLADTIVIDRAGTTEITVTALAAGEAGNTGENTLLTLITPVACVVSDAITVKGFSGGADIESAAELLSRLEYRVQYPPFGGNQFDYVRWAREVSGVTRAWCFPTWKGGGTVGVTFVMDNRSNIFPQPADVERVADYIAGHTDPITGLIVGQPDGVNVTVFAPKAKPVNPRIYISPKTAELKQAITNAINTMFFNEVMPGGALAPSRIIRAVAGVTGLDDFEVRFPTEIQRSENTELLTAGTIEWL

Entity 7 polymer

描述 description	Baseplate puncturing device gp45
分子量 formula_weight	21720.5 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	V,W,X

MERVNDSALNRLLTPLMRRVRLMLARAVVNVINDGRKVQNLQVGLLDDEESDEVERLQNYGHFSVPLPGAEALIACVGAQRDQGIAVVVEDRRYRPTNLEPGDAGIYHHEGHRIRLTKDGRCIITCKTVEVYADESMTVDTPRTTFTGDVEIQKGLGVKGKSQFDSNITAPDAIINGKSTDKHIHRGDSGGTTGPMQ

Entity 8 polymer

描述 description	Baseplate protein gp48
分子量 formula_weight	20489.1 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	a,b,c,d,e,f

MAVTPWQTAFLQLLPSGLAWNKSPDSKLSALAQAISDVIATAADDARQMLRERFPSTSRWYLGEWESFLGLPDCTSENGTLSERQRAAANKMRMTGNLSRRFYEWLAAQYGFTVRLTDSTEGQWVTQVNIYGIKNYRNATVLDNVLTPLRVYESGALECLLEKYKPAHQIYKFVYHDGDN

Entity 9 polymer

描述 description	Probable tape measure protein
分子量 formula_weight	73682.8 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	g,h,i

MTGKRLKASVIIDLNGNLSRRSRQYSNQINALSRSGQSSLRALRMEVVRVSGAIDRMGSLSTRTFRMLSAGALGIAGVGYTANKLFIGAAAQREQQIIAMNSLYHGDKVRAQAMMAWAKQNAKDTTWGLSGVLDEIRSSKGFGMTDEQTKQFITMLQDQGAMHGWDLPTAQGASLQLKQMFARQQITAADANLLTGYGINVYQALADATGTDVKKIRDLGTKGKLGMKSILTVFRTLSEQSKGAQASAMNSWDGMFAQMEANLLEFRIKVANSGPFEEIKNEMRRVLNWHDMADKSGELDALAENIGQKFLTTFRTVKISAQELWRWLKPGKDALAWVDQNIVSLKKLAAVLVSVWLANKALRAGWAVAKPSWQVASYPFKTGRRMWRWMRNRKRGQAGLPVPDAMTSETLLQGIGIQRVFVINWPRGFGDYGSGGGRRVRSGGRMAPLLPRQPLLLSGPQPLALPAPRPVLALPPPGVPVTARPAPLPLPGKSGLLSRLAGSAAGQLVTGTVGKLADAGRAVGGWFSGIGNKLAGSAIGRVVTKGAGALGWMGKGAGRALSRLGGPVMGALQLAPVLMDEQASTHEKAGAIGSTAGAWLGGAVGSLAGPLGTVAGATLGSVAGEYLGGFVTDLYQKWTATDKEPQEQKVNAEASLRVELGEGLRLTSSRVTEDGMGLNIYAGDNYITGW

Entity 10 polymer

描述 description	Tail fiber protein S
分子量 formula_weight	55412.6 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	j,k,l,m,n,o,p,q,r

MFYIDNDSGVTVMPPVSAQRSAIVRWFSEGDGNNVITWPGMDWFNIVQAELLNTLEEAGIQPDKTKLNQLALSIKAIMSNNALLIKNNLSEIKTAGASAQRTARENLDIYDASLNKKGLVQLTSATDSPSETLAATAKAVKIAMDNANARLAKDRNGADIPNKPLFIQNLGLQETVNRARNAVQKNGDTLSGGLTFENDSILAWIRNTDWAKIGFKNDADSDTDSYMWFETGDNGNEYFKWRSKQSTTTKDLMNLKWDALSVLVNAIVNGEVISKSANGLRIAYGNYGFFIRNDGSNTYFMLTNSGDNMGTYNGLRPLWINNATGAVSMGRGLNVSGDTLSDRFAINSSNGMWIQMRDNNAIFGKNIVNTDSAQALLRQNHADRKFMIGGLGNKQFGIYMINNSRTANGTDGQAYMDNNGNWLCGAQVIPGNYANFDSRYVRDVRLGTQSLTGGLSRDYKAPSGHVITGFHTNGDWEMQGGDDKVYIRPVQKNINGTWYNVASA

Entity 11 non-polymer

描述 description	CALCIUM ION
分子量 formula_weight	40.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 12 non-polymer

描述 description	FE (III) ION
分子量 formula_weight	55.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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7. 引用文献 (1)

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分辨率 resolution	3.30 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	46000

fit	/app/data/saxs_computation/ki/9ki1/9ki1.fit
pddf	/app/data/pr_computation/ki/9ki1/9ki1.pr.out
profile	/app/data/saxs_computation/ki/9ki1/9ki1.dat

Baseplate structure of Escherichia phage Mu

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 (12)

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

Entity 11 non-polymer

Entity 12 non-polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)