SAXSdb — 9k09

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	9k09
沉积日期 deposition_date	2024-10-15
最后修订 last_revision	2025-04-09
结构标题 title	Cyanophage A4 portal-tail complex
关键词 keywords	Cyanophage, Virus, Tail, Portal, Zozzle, Adaptor, Tail Fiber, 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	95.32 Å
回转半径 Rg (电子) rg_electron	94.77 Å
零角强度 I(0) i0	82925000000.00
分子量 molecular_weight	2451400.0 kDa
排除体积 excluded_volume	3058300 Å³
包络体积 envelope_volume	4751600 Å³
水化壳体积 shell_volume	394620 Å³
包络直径 envelope_diameter	318.0 Å
壳层 Rg shell_rg	103.80 Å
包络 Rg envelope_rg	92.26 Å
形状 Rg shape_rg	94.81 Å
总 Rg total_rg	94.67 Å
总原子数 total_atoms	173160
残基数 n_residues	21978
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	240.6 Å
Rg (实空间) rg_real	92.67 Å
Rg 误差 (实空间) rg_real_error	0.36 Å
I(0) (实空间) i0_real	7.9520e+10
I(0) 误差 (实空间) i0_real_error	1.4110e+09
Rg (倒空间) rg_reciprocal	97.37 Å
I(0) (倒空间) i0_reciprocal	83490000000.0000
解质量估计 total_estimate	0.9161
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	120.3 Å
偏度 Skewness skewness	0.062
峰度 Kurtosis kurtosis	-0.602
角度范围 angular_range	— – 0.0800 Å⁻¹
当前正则化参数 α current_alpha	0.9283
最高正则化参数 α highest_alpha	3917000000.0000
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: 0.000; Oscil: 0.999; Stabil: 0.972; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.000

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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	Tail fiber protein
分子量 formula_weight	39873.3 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,P,Q,R,X,Y,Z,a,b,c,p,q,r,x,y,z
原子数 atom_count	173160

MATSNVVVSRTGTGWTVDVTACNLLSDTGIKDFIVLHNAIVVSNVTYAKTTATTLTYTGAALPSNTPVEIRRKTPNSIIQLVTYGQKLSSNLWNSEIDRNIRWREEVDLNGAGLVASTPTPQNDAYGLVWAGDTFYPPTRKSVYDKIETLATKSGAVLTGATANVSPSTADNTLALATTAYVKANLADYATLVSPILTGDPRAVTTSVTDNDTSIATTAHVRAFANSRLAFNAFRGGQQGVPSLNYITTVCQFTSSAVRSGWGDNFSSNRWLVGQGGTYYVSVTCRFATTGGTPPTYMDVLLFVGLSPTGVENFVIRQQTNYPSFGYTLTWSGVLFFNTNDNVYLTYQAQAIGGGGYAVVIEDARFNAIQLS

Entity 2 polymer

描述 description	Portal protein
分子量 formula_weight	74284.6 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	D,E,F,G,H,I,J,K,L,M,N,O

MIRIKDFNHVITGREQPLDINEAIASYITSRYVYFKDARRVAEETWLEAWSLYSGTPEAVDHQRTQTINTVGEVNNDWRHRLNTGKAYECIETVHGYLMGALFPNREWFDLTPNNPGYANEARIIRKYLTKKFNEGKFRVSFEKYLRQLLVCGYSVMALPWRYESRPYKYNVTIKREENEYYDNSTQKANYRTVTENRVTRNAPEFECLDVFDVYLSPTSNDPNESDFIRRIKKTRADIITAIKRGYYTDIDPYDIVNMSAYEVNDRVDKLTSFQGIETNHPYCMDDIIEVVEYWGDLHLDGVSLYDVKATVIGQTLVCCEPNPFWAGKPFVVGSITELPETPYSVGLLQPNMGLLHQLNIITNQRCDNLELAIDEMWTLVQNSSLNPDEVQVAPGKVFLVDSHDDLRPIQRGGNNFVVSYQEAGLLESTIDRNTGTGNLISANASRSGERVTAAEIQAVRDAGGNRLSNIHRHIEDTSLMEILRRVYRSAQQFVTEPEMIRVSGAKPGEYLFLEVDPESLNKEYSLEPIGADFVTDATKYVRQRMDFIAFASQIPQMAERLNYEALLNDVVNHSGFDDPYSYIVKPQQPAPQPDMGATPEPQTGQAPPDEQTNPFYDIGGVSLQNAIGANIQADGANELINFTTGVNTNADQ

Entity 3 polymer

描述 description	Tail tubular protein B
分子量 formula_weight	113330.1 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	U,V,W,u,v,w

MTDQFERNNIRNNEVAAEQSIQSNNFGGLNTLASPLNVPYQDSPLLLNTTVDTSGQVYKRKGTRITYTTTGTSTGCYITGFTSGLAYQFQVAKRGRDILLFQTTNDVTSLLLTKSNVWDTRAEAVRPSVVTTSEVTPRVIFATGVNKPVQLLFVEQQTTQTANGTSVVFSSADRFVNASTANCLVYVNRVLVSAPSFSYNAGTKQLTVSNLGSTVIGDVIDLVSVTWQWWAESQFWYGDRFFGSTTRFNSVSFDRVVKIPTSITTQNNGSDPYYRMRLYKQSNRTGSPNLNEVVQPQLADDWAFSDGSIYNYSVNDYPNPSPFWVVFGALVGGGQPSTVYFSRRRGLGFANGTSVQASKIDVVVNGVQRTPIYTPGSAPDSVYRNYYTYFADTTGAATGTSSTSLVNGIFFDAIPLGLATNDTVEASNNTNIHIGSASIATRYNYNDGSYIPAFGLGDFADYLNGYYPSVVTFFQGRLVFGGFPHRPLQVVFSNVNDNITPGRYYNSFSITDDNTALSSAFDIILNSRPDDRVVALIEWQSSLFILTRQAVFRANGGSSILSSTNRVISYVSSNGCTNSRCIVRTDFNVMYLSDTGVYNINPLVENGEYTVKELSIKIRDKFGVTREPVYEELPWMAYDSVNKQVLLGYPDVGQTNTSRYVYVYNTYRESWTEYNTPCGFNIWSTTEYTDRLLGTSVCSILYTTTSSGTPSNFIIIRWNASLYIDFIQRKTHNGSSYELTTQPAVTHTTNVNQRRYGVNFTLTRQNTAFTINPVTTVNDLYVTLDGTLLTPNVDYIKEETGYIYLLSTFSTGQTLKIASSPEGNTTPNSWYTVYVNNIRQVSPTPSAGTFTLGATNGDIINWGVNYLTIYTTPQFLWNSLGNFKRTQHAYLFLDNRDGVGVYVASDVNNGQDINQLTELYRVPINFNLSVMYNNQLDGSTSYDVMGYDSMYWDEGVFDVSSPYDQYQPYQTLKIPITGIGYAFQMLIWNHSDEYFKLGGYQIIAKQKGKRHIGRY

Entity 4 polymer

描述 description	Tail tubular protein A
分子量 formula_weight	24783.7 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	d,e,f,g,h,i,j,k,l,m,n,o

MPKTTTFIQLVNKCLENIGERPVISFNNSVARKAADTVRDAITDVSYSYDWSWLTTSIIANSWINERADLGDVQSVKHVSYGSSSDGYRELTFTDERTFDAAKIYPGVGQVFTFNEYGGVRINPYPETVEEQVKYKFYVVKEATLPSVEIDVINIPDRFIQLITYNACTQLSISHLDDAQASQMWNSKYIDQLSRLRARERNTTQSGANMFKFRGTR

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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	—

分辨率 resolution	2.60 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	106052

fit	/app/data/saxs_computation/k0/9k09/9k09.fit
pddf	/app/data/pr_computation/k0/9k09/9k09.pr.out
profile	/app/data/saxs_computation/k0/9k09/9k09.dat

Cyanophage A4 portal-tail complex

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 (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)