SAXSdb — 8jov

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8jov
沉积日期 deposition_date	2023-06-08
最后修订 last_revision	2023-11-01
结构标题 title	Portal-tail complex of phage GP4
关键词 keywords	Complex, 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	99.03 Å
回转半径 Rg (电子) rg_electron	98.98 Å
零角强度 I(0) i0	47825300000.00
分子量 molecular_weight	1818400.0 kDa
排除体积 excluded_volume	2254900 Å³
包络体积 envelope_volume	3870000 Å³
水化壳体积 shell_volume	325040 Å³
包络直径 envelope_diameter	388.1 Å
壳层 Rg shell_rg	93.93 Å
包络 Rg envelope_rg	97.81 Å
形状 Rg shape_rg	99.06 Å
总 Rg total_rg	98.68 Å
总原子数 total_atoms	128070
残基数 n_residues	16764
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	267.1 Å
Rg (实空间) rg_real	94.49 Å
Rg 误差 (实空间) rg_real_error	0.93 Å
I(0) (实空间) i0_real	4.5690e+10
I(0) 误差 (实空间) i0_real_error	9.3240e+08
Rg (倒空间) rg_reciprocal	95.80 Å
I(0) (倒空间) i0_reciprocal	47300000000.0000
解质量估计 total_estimate	0.9102
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	100.1 Å
偏度 Skewness skewness	0.388
峰度 Kurtosis kurtosis	-0.531
角度范围 angular_range	— – 0.0800 Å⁻¹
当前正则化参数 α current_alpha	0.6838
最高正则化参数 α highest_alpha	16450000000.0000
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: 0.015; Oscil: 0.960; Stabil: 0.986; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.009

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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 (5)

Entity 1 polymer

描述 description	Portal protein
分子量 formula_weight	87929.2 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	0,3,6,U,Y,c,g,k,o,r,u,x
原子数 atom_count	128070

MFDLRDDQNTRVIADHPEARMPTEEPGKDDAPPSHPLDSEEMKELHRRLRSYLHQELDRQAENRFQMAVDEDYYDSIQWTEADAQVLKERGQAPLVFNVIAQSVNWIIGSEKRGRTDFNILPRKKADAKPAEAKTKLLKYLSDVNRLPFHRSRSFEDTVKVGLGWIEDSYDDSTDGEPIYSRYESWRNVIFDSASTELDGTDMRYIFRPKWLDVDVACALVPDRADEIKKAAVAAERYGNYSEEDGDEAMDWAEFDRDTYSQSRTVSTHKRQRVRLIECWYRKPMRATKFLSGDLRGETLDESNPAHVEARDSGLYSLGERITMRVRVAIFTSRDLLFEGASPFRHNRFSLTPIWGFRRGRDNLPYGVIRWMRDIQDDINKRASKALYILSSNKVVMDEGAVEDIEEFREEVARPDAVLVKKPGKQIELNVDRELAAAHMDMMSRDIQMLQQVGGVTDELMGRSTNAVSGVAIQARQEQGTVATNKLFDNLRFAVQMQGEIQLSLIEQFVTEEKTFRITNERGKADFITVNDGLPENDIVRTKADFIIGESDWRATYRQAASEQLSQMIMKMPPQVGLVMLDLWADSTDLPNRDEIVKRIRQINGMRDPDATEPTPEELQQQQAAAEQAQAQKAMFMAELSEKQGKADKAQADAVAAQANADLRAAQAEQVRRQTVNTNVTSIAAAMEAATAIVTMPTIAKVGDAVLVEAGYENNGIAPAGGLHTPAPQQAVNPAAQGLPPQQPQPQQPQEPAVSPSPEQLNGAAPSNTGEPVTPDQTLQQ

Entity 2 polymer

描述 description	Putative tail fiber protein
分子量 formula_weight	45894.8 kDa
来源方法 src_method	nat
拷贝数 entity_count	18

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	1,4,7,M,N,O,P,Q,R,V,Z,d,h,l,p,s,v,y

MAAVQFANNAASRLVGPLAPSGTSLTVTPGDGALFPTLGAGDWFMATLIRSDGAREIVKVTSRTVDAMSITRAQEGSSALSFNPNDRIEARLTAGELGDFRDGIASAQSAASAAQGTADGKISKAGDTMTGNLNMEGAAPIITFRETDQAAPAGRWRLVADGGNWSLRRSTAGEFASENSTMWFGPDDSVHFLNDILIGRGNLGSVYDALASKATSAALASGLSAKPDADGVSVTGFVNGNFYEPYFRKSSDNTVRRLVANTSANGIALSWSGSFLSRTIDNTATATIWDTANAPGAGTTNLDKTFYCGDGTRIGRSWVPGSGFLSITVDGTNYGISISASDERLKREIAPSEASALSKLGRIELFSFRYKEGNAFLDPSQHHDIGFIAQQLASVDPTFVAGGGETMLSPNLQPIVATLVKAVQELRSQVDALKAQVGA

Entity 3 polymer

描述 description	Virion associated protein
分子量 formula_weight	23545.3 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	2,5,T,X,b,f,j,n,q,t,w,z

MAFPASVVLSRAATLLQDEDHERWTVDELLEWLTDGTREIVVRKPSAYMKTTTAALVAGSKQALPEDAIQLIDVPRNLKTDGSPGRAVTATDRRLLDTENPDWHSMKPAGQIRHYTYDSNVPTVFYTYPPAAAGVQVELVCAWRHPALTTQNDVVQMGAEFVSALVSWCLYRASSKDSEFANGAVAAAHYSAFSDALGAQATGTPTTQAAAAAAAAGAAQ

Entity 4 polymer

描述 description	Virion-associated phage protein
分子量 formula_weight	62764.6 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

MTTLKLTAYSGEVPRTLPRLLPDTASQRALNVRLDNGGLTPTRQPRFEANISVDNAKTIYKHNGAWLAWQNVVHAAPGPVAQDRLYYMGDGKPKMIVDGTTYDLAVPMPTAAPALTVTGTGTGNVTSIAYVYTFVTAFGEESEPSALSNVAGWQSGQTRTLTGIQAPPAGRNITKQRFYRSQTGSGGTDLFFIEERAASAANFVDTHATNDFGEMLPSLEYNAPPDGLKGLISLPNGMMAAFTGKDLYFCEPFIPHAWPEKYILTMDYQIVALGAYGTTIVVMTEGLPYIVSGTAPENMQQQRVELNLPCINARGVIDLGYSVAYPSHDGLVMAGSNGMQVITEQLMTRNDWMKTGPGNIVGGQFNGRYFASYEYIEPSGAAFSGTLIFDTTGAAPFIIRSNHKADAFFHELQTGALYFLVGKEIFEWDALGQVNETLSWRSKQFVLPMPTNFGAILIEGSTAASEEEQAAYDAERQRIEVENATNFALPSIGGEMNGAEVNLFAVNGDMMQRLPAEGFVSVSIYADGKLVKTVSKMNRMARLPSGFLARIWEIEVNSNINISDIVLATTGQELRNV

Entity 5 polymer

描述 description	gp81 of phage GP4
分子量 formula_weight	23197.4 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	G,H,I,J,K,L,S,W,a,e,i,m

MKPLDVFMPIIHRFAPGCPEPTAFAAIREAAIKFCERTRLWRCDDEFNVGADECAEVAVPYGAALYEMELVQFNGRNMRPVSTQWLDEQVPDWRTTTQSGQAQYVTQQSEDTLTFVPAEAGSVRVYGLLKPTLDADSLPDLLADTYRKTIADGALSELLIIPGKAWMSADLAVFFGTRFDRELDRLSTKTIKGQQRAPVRTRAQFF

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7. 引用文献 (1)

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分辨率 resolution	3.80 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	39883

fit	/app/data/saxs_computation/jo/8jov/8jov.fit
pddf	/app/data/pr_computation/jo/8jov/8jov.pr.out
profile	/app/data/saxs_computation/jo/8jov/8jov.dat

Portal-tail complex of phage GP4

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 (5)

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

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)