SAXSdb — 9jyz

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	9jyz
沉积日期 deposition_date	2024-10-13
结构标题 title	portal-tail complex of mature T7
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	86.01 Å
回转半径 Rg (电子) rg_electron	85.93 Å
零角强度 I(0) i0	45930400000.00
分子量 molecular_weight	1803600.0 kDa
排除体积 excluded_volume	2245900 Å³
包络体积 envelope_volume	3241000 Å³
水化壳体积 shell_volume	302440 Å³
包络直径 envelope_diameter	319.8 Å
壳层 Rg shell_rg	90.68 Å
包络 Rg envelope_rg	85.20 Å
形状 Rg shape_rg	85.91 Å
总 Rg total_rg	86.05 Å
总原子数 total_atoms	126948
残基数 n_residues	16140
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	234.5 Å
Rg (实空间) rg_real	81.73 Å
Rg 误差 (实空间) rg_real_error	0.72 Å
I(0) (实空间) i0_real	4.3780e+10
I(0) 误差 (实空间) i0_real_error	7.9190e+08
Rg (倒空间) rg_reciprocal	85.46 Å
I(0) (倒空间) i0_reciprocal	45860000000.0000
解质量估计 total_estimate	0.9112
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	104.2 Å
偏度 Skewness skewness	0.297
峰度 Kurtosis kurtosis	-0.320
角度范围 angular_range	— – 0.0900 Å⁻¹
当前正则化参数 α current_alpha	0.6261
最高正则化参数 α highest_alpha	3420000000.0000
实空间数据点数 n_real_points	19
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.964; Stabil: 0.981; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.012

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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 (6)

Entity 1 polymer

描述 description	Protein 6.7
分子量 formula_weight	9354.5 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	0,3,4,5,6,7,8,9,AA,AB,AC,AD
原子数 atom_count	126948

MCFSPKIKTPKMDTNQIRAVEPAPLTQEVSSVEFGGSSDETDTEGTEVSGRKGLKVERDDSVAKSKASGNGSARMKSSIRKSAFGGKK

Entity 2 polymer

描述 description	Protein 7.3
分子量 formula_weight	10088.7 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	1,2,v,w,y,z

MGKKVKKAVKKVTKSVKKVVKEGARPVKQVAGGLAGLAGGTGEAQMVEVPQAAAQIVDVPEKEVSTEDEAQTESGRKKARAGGKKSLSVARSSGGGINI

Entity 3 polymer

描述 description	Tail fiber protein
分子量 formula_weight	61641.9 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	A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,a,b,c

MANVIKTVLTYQLDGSNRDFNIPFEYLARKFVVVTLIGVDRKVLTINTDYRFATRTTISLTKAWGPADGYTTIELRRVTSTTDRLVDFTDGSILRAYDLNVAQIQTMHVAEEARDLTTDTIGVNNDGHLDARGRRIVNLANAVDDRDAVPFGQLKTMNQNSWQARNEALQFRNEAETFRNQAEGFKNESSTNATNTKQWRDETKGFRDEAKRFKNTAGQYATSAGNSASAAHQSEVNAENSATASANSAHLAEQQADRAEREADKLENYNGLAGAIDKVDGTNVYWKGNIHANGRLYMTTNGFDCGQYQQFFGGVTNRYSVMEWGDENGWLMYVQRREWTTAIGGNIQLVVNGQIITQGGAMTGQLKLQNGHVLQLESASDKAHYILSKDGNRNNWYIGRGSDNNNDCTFHSYVHGTTLTLKQDYAVVNKHFHVGQAVVATDGNIQGTKWGGKWLDAYLRDSFVAKSKAWTQVWSGSAGGGVSVTVSQDLRFRNIWIKCANNSWNFFRTGPDGIYFIASDGGWLRFQIHSNGLGFKNIADSRSVPNAIMVENE

Entity 4 polymer

描述 description	Tail tubular protein gp12
分子量 formula_weight	89480.6 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	P,Q,R,S,T,x

MALISQSIKNLKGGISQQPDILRYPDQGSRQVNGWSSETEGLQKRPPLVFLNTLGDNGALGQAPYIHLINRDEHEQYYAVFTGSGIRVFDLSGNEKQVRYPNGSNYIKTANPRNDLRMVTVADYTFIVNRNVVAQKNTKSVNLPNYNPNQDGLINVRGGQYGRELIVHINGKDVAKYKIPDGSQPEHVNNTDAQWLAEELAKQMRTNLSDWTVNVGQGFIHVTAPSGQQIDSFTTKDGYADQLINPVTHYAQSFSKLPPNAPNGYMVKIVGDASKSADQYYVRYDAERKVWTETLGWNTEDQVLWETMPHALVRAADGNFDFKWLEWSPKSCGDVDTNPWPSFVGSSINDVFFFRNRLGFLSGENIILSRTAKYFNFYPASIANLSDDDPIDVAVSTNRIAILKYAVPFSEELLIWSDEAQFVLTASGTLTSKSVELNLTTQFDVQDRARPFGIGRNVYFASPRSSFTSIHRYYAVQDVSSVKNAEDITSHVPNYIPNGVFSICGSGTENFCSVLSHGDPSKIFMYKFLYLNEELRQQSWSHWDFGENVQVLACQSISSDMYVILRNEFNTFLARISFTKNAIDLQGEPYRAFMDMKIRYTIPSGTYNDDTFTTSIHIPTIYGANFGRGKITVLEPDGKITVFEQPTAGWNSDPWLRLSGNLEGRMVYIGFNINFVYEFSKFLIKQTADDGSTSTEDIGRLQLRRAWVNYENSGTFDIYVENQSSNWKYTMAGARLGSNTLRAGRLNLGTGQYRFPVVGNAKFNTVYILSDETTPLNIIGCGWEGNYLRRSSGI

Entity 5 polymer

描述 description	Tail tubular protein gp11
分子量 formula_weight	22307.7 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	U,V,W,X,Y,Z,d,e,f,g,h,i

MRSYDMNVETAAELSAVNDILASIGEPPVSTLEGDANADAANARRILNKINRQIQSRGWTFNIEEGITLLPDVYSNLIVYSDDYLSLMSTSGQSIYVNRGGYVYDRTSQSDRFDSGITVNIIRLRDYDEMPECFRYWIVTKASRQFNNRFFGAPEVEGVLQEEEDEARRLCMEYEMDYGGYNMLDGDAFTSGLLTR

Entity 6 polymer

描述 description	Portal protein
分子量 formula_weight	59174.0 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	j,k,l,m,n,o,p,q,r,s,t,u

MAEKRTGLAEDGAKSVYERLKNDRAPYETRAQNCAQYTIPSLFPKDSDNASTDYQTPWQAVGARGLNNLASKLMLALFPMQTWMRLTISEYEAKQLLSDPDGLAKVDEGLSMVERIIMNYIESNSYRVTLFEALKQLVVAGNVLLYLPEPEGSNYNPMKLYRLSSYVVQRDAFGNVLQMVTRDQIAFGALPEDIRKAVEGQGGEKKADETIDVYTHIYLDEDSGEYLRYEEVEGMEVQGSDGTYPKEACPYIPIRMVRLDGESYGRSYIEEYLGDLRSLENLQEAIVKMSMISSKVIGLVNPAGITQPRRLTKAQTGDFVTGRPEDISFLQLEKQADFTVAKAVSDAIEARLSFAFMLNSAVQRTGERVTAEEIRYVASELEDTLGGVYSILSQELQLPLVRVLLKQLQATQQIPELPKEAVEPTISTGLEAIGRGQDLDKLERCVTAWAALAPMRDDPDINLAMIKLRIANAIGIDTSGILLTEEQKQQKMAQQSMQMGMDNGAAALAQGMAAQATASPEAMAAAADSVGLQPGI

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7. 引用文献 (1)

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晶胞边长 a length_a	1.000 Å
晶胞边长 b length_b	1.000 Å
晶胞边长 c length_c	1.000 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.00 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	—

空间群 space_group	P 1
空间群编号 int_tables_number	1
晶系 crystal_system	triclinic

分辨率 resolution	2.70 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	65620

fit	/app/data/saxs_computation/jy/9jyz/9jyz.fit
pddf	/app/data/pr_computation/jy/9jyz/9jyz.pr.out
profile	/app/data/saxs_computation/jy/9jyz/9jyz.dat

portal-tail complex of mature T7

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

晶胞参数 Unit Cell

对称性 Symmetry

冷冻电镜 EM 3D

5. 实体与聚合体信息 (6)

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

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)