9ndy

Composite baseplate asymmetric unit of JohannRWettstein (Bas63)

Method: ELECTRON MICROSCOPY D_max: 219.6 Å Quality: GOOD

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

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	9ndy
沉积日期 deposition_date	2025-02-18
结构标题 title	Composite baseplate asymmetric unit of JohannRWettstein (Bas63)
关键词 keywords	;baseplate, wedge, hub, puncture apparatus, sheath initiator, tube initiator, tape measure protein, LTF-platform, spacer, phage, bacteriophage, VIRAL PROTEIN ;; VIRAL PROTEIN
实验方法 method	ELECTRON MICROSCOPY

▼

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	64.50 Å
回转半径 Rg (电子) rg_electron	62.62 Å
零角强度 I(0) i0	2851700000.00
分子量 molecular_weight	427680.0 kDa
排除体积 excluded_volume	526230 Å³
包络体积 envelope_volume	1001000 Å³
水化壳体积 shell_volume	133160 Å³
包络直径 envelope_diameter	222.1 Å
壳层 Rg shell_rg	64.71 Å
包络 Rg envelope_rg	61.53 Å
形状 Rg shape_rg	62.76 Å
总 Rg total_rg	62.21 Å
总原子数 total_atoms	30166
残基数 n_residues	4160
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

▼

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	219.6 Å
Rg (实空间) rg_real	64.31 Å
Rg 误差 (实空间) rg_real_error	1.91 Å
I(0) (实空间) i0_real	2.8520e+09
I(0) 误差 (实空间) i0_real_error	6.0690e+07
Rg (倒空间) rg_reciprocal	64.63 Å
I(0) (倒空间) i0_reciprocal	2853000000.0000
解质量估计 total_estimate	0.8592
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	82.3 Å
偏度 Skewness skewness	0.270
峰度 Kurtosis kurtosis	-0.298
角度范围 angular_range	— – 0.1200 Å⁻¹
当前正则化参数 α current_alpha	0.0003
最高正则化参数 α highest_alpha	245000000.0000
实空间数据点数 n_real_points	25
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.810; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.970; Smooth: 0.765

▶

4. 晶体学与实验 4. Crystallography & Experiment

▶

5. 实体与聚合体信息 (9)

Entity 1 polymer

描述 description	Tube initiator protein (gp018)
分子量 formula_weight	28593.9 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	30166

MLWDSNMQIKYSGKDGIYFHLRDNVDAFLTLSATENMEFDSPMQVTTQNMQSGQTVTDNVQRAPRTITISGVVVVGYEGSLLLTRQGQLVENFIDTLESWRDQKQIISVICKDGIKIDDSIITSFKASKDVGISNGLRVQLTFQEINFKAIVGQTDVSAATGKTATTNDGGATSKKNTGNTTTSLGNGKLNCQLLFDLDANGVRELTSAEDNALAKCSMSAKTRKGVTTFSDEAERNAGAALNSTAGNGKALQKHSVNPNKKGTY

Entity 2 polymer

描述 description	Sheath initiator (gp022)
分子量 formula_weight	15632.6 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	C,D

MKTDFALNLGGDYVATLGSDSVYVAHGDLKITGNQIRIIPEDDKATQVAQRLHIRCLLRSGEVFFNTSAGFPYLQLAKFKQKTSIFDNYMKAYLVETRDVSNIYNYSSSMDNAQRKVTVNFDATTTTDILTDITQEVNI

Entity 3 polymer

描述 description	Hub protein (gp020)
分子量 formula_weight	37204.2 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	E

MSVKDSTAGASFRCYQLAVGSETTAFNDKPTSHAKDSMQMDYFDNLQFTCNVSYTSQKNKVTSDDTTFEIYNLNKEMRAKFKTVGATVMLRAGYTTGFKRDANGDLIIEYDNLPLIYLGTIEYAYTYKRGVDMITKVICSNDKMERTTIKTSISYKAGTTRKNVIRDLVNRLGFSLIDEDLSSIDGYTYKNGFSVWGSVAEALTKVCEESSLRWYTFNKQIRVVPFNAKARQLSWEIYPYNVIDSLQGYYRRTRKVLKKENKTVIKVKTGVRCKIHLDGRIKMGDNVTIRESEDFEGQYRVKGLSHNLDFTGGAWTTELDLEKVE

Entity 4 polymer

描述 description	Tape measure protein (gp017)
分子量 formula_weight	80340.6 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	F

MAQYTVDSFIVELGFSEKVVKGLQRVEKMSMQAAQRIERNINKAFDVKPNKSSQEALNRIVKNAQSASGRINKALNSSLNLDSQGVKSLKKLETQAKKTAKGINKSLRDAMKVDGKITIKTGRGRGGQSIPPVGGGAPRGPRVDVAQRQMERMFNNNFYSGLTRRLETIGGQGNQMAASFRGSLQGIYNKYKGTGKVGEYEMEVKKLIDVTKRWVIAENARLKSVKEAAWLQDRANSSLRQLVGGFVSAYALLELSQKTIEAGVKRQSAQLASTAIFGADTQQARMFAASFAHQIGQNYTDTMKQYSNFAAGAQPTLGFQGTQEFYKNAAMFARIRGATDEDLKGIMVAFQQMASKGKVQAEELRGQLGDRLAGAVQLFADAIGKTPQELDKMMQDGKLLAQDVLPKVSERMAELVKQAGGMNAVSKQTATSMGQAKAMWDNTLVALFNNSSEGISQLSNSVAMFLQGSLGSTQALGVVIGNLLKGASNLLDFVTDFMYRTSALYYYARAWYKDLDNSQQKLIKSAGEFLGTVVTIGGVVAVVSKAVKLLSGLVGGGIFGKILQRLGVSAAGTAAAGEAAAAAGGVTATRMALGTVGSALMLRGSTDPNAAKNYSEVTLPKPFENAVANITNPKRPMFFDENGQLQFAQYTQDVEGNRKLIDNGLSNWEIIMDKLSTSIDNFANKFNQTPMMMTPSGLPMQTKQTLNVTFNLDGKQIATKMVDITDKNQEDILLSSSYPEEE

Entity 5 polymer

描述 description	Puncture apparatus (gp021)
分子量 formula_weight	23186.8 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	G

MKSPVTRMSGYVSECLDEFRKELYTGLPAIIQSFDSKTQTATVKPLYSINGLPMPEITGVPVQFPSGGGASLTFPVKTNDRCWLAFSMLPLDDFVVNDKNTQMETNMRRTHDISDCVAFVGICTRTQNFKPDPTAVRLHFGDSVLRVTDDGNFYFEGDVHISKNLYVKEEVHGSDFISDTTGVSFNEHTHHYYWTDPAGEADTTEAQ

Entity 6 polymer

描述 description	Wedge protein 2 (gp023)
分子量 formula_weight	53140.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	H,I,K,L

MAGLTTTGLQTLRYQEIFDNIKSRLLRDISPNLDVSEDSQLGLFLASIARSLADTHEVLSEIYDGGTIDKAEGFNLDDITALNAVYRYVAQATRGQVEFTGTTGATIPSTTRLRSTAGNIFYPVSGITLTPSYCVEAVLEVNSLRTDANYVIIIDNVIFSYQPKSSDTITVLLTELADAINGGIVAKAEVINDGSALRVYKDEGDIIARTNPMVVTATTFLTFTKITTIHDVVAEEVGAIPALAGTLIEIETTVDGLDSVYNRYDLTTGRNEETDTELRQRYLESLAVTGVGTLDAIVAAVKRVQGVSDASGVENDTEETSSEGLPPKSFKIVVVGGQNDNVAQAIWDTKPAGIRAYGAIFGTAYDLGNLAHNVYFSRPTPKYAFVKVSYSLYDEESLTIPEEDIRDSIVQGINAYGRTLKVGNDVIPNRIYGYIYDVIKGVEINEIKVALSNNQSVPPSDGQYTTARITVDGDQYTVWESSQYTIAKE

Entity 7 polymer

描述 description	Wedge protein 1 (gp024)
分子量 formula_weight	31622.6 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	J,M

MFQKIDNVYYKTLDERTVTQFKDKFIYTSLLKAVTDELQTLEDVSWQMHTERNIRKAVGQQLDNIGSLIKVPRPLGADDETYRAMLYIQIFLRRSDTTPTFLQNAIMTLYNATFSQIFEHITPMTAGIVVRVNTRNNVIDTAYTLAKIAATTIGSAVILRDVTLNGTAWTPVEVADSALAIVDDKDNWFVTDANKGLVTNNTGGSLEKNLLGSLADAGVRDAYFKVDRTANSGSVDYLKVNKNYNATDNYIVGKETVAGGDYGVMAEVAQIIKGRKDKSQQEGSS

Entity 8 polymer

描述 description	Spacer protein (gp019)
分子量 formula_weight	13209.9 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	N,O

MSQYIPVPDTEWSTQTVTLDGTVFVIELKYKERLDRWFLTLSDVDGNVLLSEKKCLADQSITGRYVIPSLAGELFVERMYGTDLQPTRNNFGREKAFELNYYTQEDMRLMENL

Entity 9 polymer

描述 description	LTF platform protein (gp025)
分子量 formula_weight	11093.4 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	S,T,U,P,Q,R

MAFLNWSTDEVDADGNQLKVLPPPEIQATGLLRGEPMGRQWFNYILNYLLKKANGTVGEVRSFATEQPDLVANGWNLIKTETGTASTSTKNLYTYEFVGA

▶

7. 引用文献 (1)

▶

分辨率 resolution	3.83 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	14390

fit	/app/data/saxs_computation/nd/9ndy/9ndy.fit
pddf	/app/data/pr_computation/nd/9ndy/9ndy.pr.out
profile	/app/data/saxs_computation/nd/9ndy/9ndy.dat

Composite baseplate asymmetric unit of JohannRWettstein (Bas63)

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 (9)

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

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)