SAXSdb — 8i4m

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8i4m
沉积日期 deposition_date	2023-01-19
结构标题 title	Portal-tail complex structure of the Cyanophage P-SCSP1u
关键词 keywords	Whole virus, Capsid, cyanophage, T7-like virus, 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	91.27 Å
回转半径 Rg (电子) rg_electron	90.98 Å
零角强度 I(0) i0	51649000000.00
分子量 molecular_weight	1910800.0 kDa
排除体积 excluded_volume	2380300 Å³
包络体积 envelope_volume	4006100 Å³
水化壳体积 shell_volume	349360 Å³
包络直径 envelope_diameter	347.8 Å
壳层 Rg shell_rg	97.28 Å
包络 Rg envelope_rg	91.08 Å
形状 Rg shape_rg	90.98 Å
总 Rg total_rg	91.04 Å
总原子数 total_atoms	134400
残基数 n_residues	17436
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	241.8 Å
Rg (实空间) rg_real	86.77 Å
Rg 误差 (实空间) rg_real_error	0.51 Å
I(0) (实空间) i0_real	4.9080e+10
I(0) 误差 (实空间) i0_real_error	8.3400e+08
Rg (倒空间) rg_reciprocal	91.14 Å
I(0) (倒空间) i0_reciprocal	51630000000.0000
解质量估计 total_estimate	0.9093
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	99.5 Å
偏度 Skewness skewness	0.233
峰度 Kurtosis kurtosis	-0.418
角度范围 angular_range	— – 0.0850 Å⁻¹
当前正则化参数 α current_alpha	0.6502
最高正则化参数 α highest_alpha	5487000000.0000
实空间数据点数 n_real_points	18
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.002; Oscil: 0.978; Stabil: 0.965; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.001

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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	Portal protein(gp 16) of the cyanophage P-SCSP1u
分子量 formula_weight	62460.4 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	S,T,U,V,W,X,Y,Z,a,b,c,d
原子数 atom_count	134400

MKTRLTNNVDRQSALYGSSGGTAAQRYEQLRVDRNSPLKRARDCSKVTIPGLIEDENYGDAGRLDTPYQSSGARGVGHMTSKLAVTLFPTNEHFFKLEIDSLAILASDQNPEMITEFDSALVKVEQAVMRMFETIGGRAAMHEALKHLLVGGNVLLYVSDEGIKVIHLDSYVLCRDPMGNVTEIVVEEEIFKDALPEEYLDEEDDDDDDMGKKMVKIYTCIKFMDDQCHWYQEIKGKEVPGTHGKCAADVAPWIALRQDRVDSEMYGRSYVEQYYGDLLALENLYKAILEASASLSKVLFLCNPNGTTRPRTLSQASNGSIVQGNAADVTVLQAAGKSQDLQIANQTIERIENRLAFAFMLNTAIQRPGERVTAEEIRYMAQELDAGISGLYSILSRELQLPLVRRLIHILRRKRKLPDFPRSEVTGEPLIKEKAVTGIEAIGRGDDRNKLIDFITTANQALGPQAMTQFLNVEEALRRLAASGSIDTTNLVKTKAQLQQEAAAQAEAEQQAQQQQLLETGIKSPAMAQAVKNFQGADPERAAQALSAITSETGGIDADQLTEAV

Entity 2 polymer

描述 description	Nozzle protein(gp 23) of the cyanophage P-SCSP1u
分子量 formula_weight	87444.9 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

MPLISSSIPNLINGVSQQPAALRLASQAEEVINCMPSPVEGLKKRPPMQHIKKLFAGSAGTGRPFTHIVDRDGVIRYLIFIQDNAIKVFDLDGNAQTVSTPNGTSYLNITGEPSSTFRVASIADFTFIVNREKTVAMDTTNKSYNWGTKSMVFIKSADFSTTYRVKLNGTEKSVTTGNSSGSAPDTVTIASDLATQLNTISGFTVTSTDYIIRITKDDGGDYTLESSDTKTADATSAIKGTVDSITDLPTIAEHNFTVRIQGSATTAFDDYFVKFEATAGSGFGPGVWRETVAPNIDHLLDKSTMPHTLVRNANGTFTFAQFNYTGRVAGDTTTAPNPTFVGSKIKNINLFRNRLVFLADENVILSAADSFERFFPETVQTLLDSDPIDISSGGTSVNFLNSSLAFANTLLLFSLHGQFRLDTGSTSVGTALTPKTATITAITTFDIVDAIDPIGVGRTVYFGIPKGDFSGLREYFLPDASGPIPLSEEVTSSVPRFVPGNLISMSPSVSEEVITMISKDQPRRVYIYKFFFDDDQKLQSSWSYWEVAANKTLLGGNVLDSDLYTCVEYSDGVYLEKTQLRPETVDSGTEFEILLDRKTTEAACSTSLINSGALGVQTVITLPYPMSGTGTMAVVGRFASNNTIAHGQVIKATAETLTGGASGNGTMTVPGDLSSAKFFVGEIYNMTYEFSTPYLKETPPGGGLAVLANPRLQLRTWSIVFDETSNFSMKITPGQRDELTYPFNGYKIGSGQFPIGTPSLATGRFRVPVMAQNIETKIVLFSDSPLPCRVQSAEWEGWYQERARRL

Entity 3 polymer

描述 description	Adaptor protein(gp22) of the cyanophage P-SCSP1u
分子量 formula_weight	22811.5 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	G,H,I,J,K,L,q,r,s,t,u,v

MAARTSFLDAVNRVLQMLGEAPVNSLQGQFGLAKQAEVALNDVSRTIQTEGWSFNTDLEKKLERNSSNEIELSSNVSRVVVDNLEYPDIDVVQRGDKLYDRKNNRYTFDEDLIVDMTTILEWDLLPEHARQYITIKAGRQLQEAIIGSAELTKLNLTQEVEARSAFLEEETTKSEHSMLRGHLNRTSPVNTYIPSRTLER

Entity 4 polymer

描述 description	Fiber protein(gp 28) of the cyanophage P-SCSP1u
分子量 formula_weight	113856.6 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	e,f,g,h,j,l,i,k,m,n,o,p,M,N,O,P,Q,R

MAFAQRIITSNSAGDQEFTFTFDYIKEEHIKVFVNFVEKAQGTGSNEFQVITNTTPKKISLNTGLSADNTRVEIRRVSSLSTPLVDFADGSTLTAADLDTAEKQSLFIDQELDDALKQGISIDTSTGVPTLNSQRLSNVSDPVNAQDAVTKAYLERSGSITSTQILNGTIVDADINASAAIAKSKLAALNIVNADVNASAAIAGSKLADASIAYTKIQNVSATNRILGRDSSGAGVIEEITPANLRTMINVEDGATADQSAAEIRTLVESASDSNVFTDADHTKLNAIEASADVTDATNVDAAGAVMNSDTSTAAMQFVIDEDTFGSNLDTKVPTQQSVKAYITATSQPLDSELSQLAGMQSGTASKLADSTALTADIADLNQLDGMAKETSITNSNTKFPTSAAVVNFVANQIAPVGGLEVIADEDSFPATQPVSGVVISISNADGLVINNAGEASNARTVGSGSDNVTIKNFPASLRNQTLAPNLGLLVSSTGASQEYNYHKLLAKETDVLQLSDDINDFNNRYRVENTLPAANDSSNHDGDLVYAKEEKKIYVYSGDYNGTPVGSFGEVQSIGNFFISTLSPAFNGSLQDFTITNAPSNAQQIILSINGVIQKPNSGTSTPSEGFALSGSTIKLAAAPPSGADYFAIVLGSTVNIGTPSNNTVTSSILQNGSVIEAKLGSGAVTRTKLNLVSTSSAPGLEVKGDGSSDGYLQLNCSQNSHGIKLKSPPHSAGQSYTLTFPSNIVSGQFLTTDANGNLSWAAVVTDLVNDTSPQLGGNLDCNDKNILLNDSSGSANNRIRLGASQDFALFHNGTINIIEAVSGDLHLRLNGSEEGIIVKQNGAVELYYDNSKKFHTSSVGATVTGNLFLSGGYINLNDNYSYGMGSGNRAQLYHSGNHQYLLNTVGNMYFQPKSGENGIVIIPDDAVELYHNNVKRLETTSGGVTVSGSVTATGHLFVGANTHYLYFTSTAGYSPRIGNADGGTGVNMTFHTNNTMRMMLQNDGHLRPASNNTYDLGTSSDRWRNVYTNDLNLSNEGGANDVDGTWGSYTIQEGAEDLFLINKRTSKKYKFNLTEVS

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7. 引用文献 (1)

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分辨率 resolution	3.81 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	86469

fit	/app/data/saxs_computation/i4/8i4m/8i4m.fit
pddf	/app/data/pr_computation/i4/8i4m/8i4m.pr.out
profile	/app/data/saxs_computation/i4/8i4m/8i4m.dat

Portal-tail complex structure of the Cyanophage P-SCSP1u

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 (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)