8r69

Neck and tail of phage 812 virion (composite)

Method: ELECTRON MICROSCOPY D_max: 285.6 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

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8r69
沉积日期 deposition_date	2023-11-21
结构标题 title	Neck and tail of phage 812 virion (composite)
关键词 keywords	phage, neck, connector, tail, 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	— Å
回转半径 Rg (电子) rg_electron	106.40 Å
零角强度 I(0) i0	2584920000.00
分子量 molecular_weight	432060.0 kDa
排除体积 excluded_volume	541540 Å³
包络体积 envelope_volume	1128800 Å³
水化壳体积 shell_volume	106130 Å³
包络直径 envelope_diameter	388.9 Å
壳层 Rg shell_rg	66.09 Å
包络 Rg envelope_rg	103.10 Å
形状 Rg shape_rg	106.40 Å
总 Rg total_rg	105.90 Å
总原子数 total_atoms	30444
残基数 n_residues	3805
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	285.6 Å
Rg (实空间) rg_real	96.62 Å
Rg 误差 (实空间) rg_real_error	1.76 Å
I(0) (实空间) i0_real	2.4730e+09
I(0) 误差 (实空间) i0_real_error	5.0880e+07
Rg (倒空间) rg_reciprocal	90.10 Å
I(0) (倒空间) i0_reciprocal	2478000000.0000
解质量估计 total_estimate	0.8631
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	57.1 Å
偏度 Skewness skewness	0.426
峰度 Kurtosis kurtosis	-0.814
角度范围 angular_range	— – 0.0750 Å⁻¹
当前正则化参数 α current_alpha	0.6713
最高正则化参数 α highest_alpha	65130000.0000
实空间数据点数 n_real_points	16
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.002; Oscil: 0.839; Stabil: 0.971; Sysdev: 1.000; Positv: 1.000; Valcen: 0.809; Smooth: 0.003

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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 (9)

Entity 1 polymer

描述 description	Capsid protein
分子量 formula_weight	15943.0 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	T,U
原子数 atom_count	30444

MASEAKQTVHTGNTVLLMIKGKPVGRAQSASGQREYGTTGVYEIGSIMPQEHVYLRYEGTITVERLRMKKENFADLGYASLGEEILKKDIIDILVVDNLTKQVIISYHGCSANNYNETWQTNEIVTEEIEFSYLTASDKART

Entity 2 polymer

描述 description	Major tail sheath protein
分子量 formula_weight	64559.0 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	V,W

MAVEPFPRRPITRPHASIEVDTSGIGGSAGSSEKVFCLIGQAEGGEPNTVYELRNYSQAKRLFRSGELLDAIELAWGSNPNYTAGRILAMRIEDAKPASAEIGGLKITSKIYGNVANNIQVGLEKNTLSDSLRLRVIFQDDRFNEVYDNIGNIFTIKYKGEEANATFSVEHDEETQKASRLVLKVGDQEVKSYDLTGGAYDYTNAIITDINQLPDFEAKLSPFGDKNLESSKLDKIENANIKDKAVYVKAVFGDLEKQTAYNGIVSFEQLNAEGEVPSNVEVEAGEESATVTATSPIKTIEPFELTKLKGGTNGEPPATWADKLDKFAHEGGYYIVPLSSKQSVHAEVASFVKERSDAGEPMRAIVGGGFNESKEQLFGRQASLSNPRVSLVANSGTFVMDDGRKNHVPAYMVAVALGGLASGLEIGESITFKPLRVSSLDQIYESIDLDELNENGIISIEFVRNRTNTFFRIVDDVTTFNDKSDPVKAEMAVGEANDFLVSELKVQLEDQFIGTRTINTSASIIKDFIQSYLGRKKRDNEIQDFPAEDVQVIVEGNEARISMTVYPIRSFKKISVSLVYKQQTLQA

Entity 3 polymer

描述 description	Portal protein
分子量 formula_weight	64155.7 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

MADLFKQFRLGKDYGNNSTIAQVPIDEGLQANIKKIEQDNKEYQDLTKSLYGQQQAYAEPFIEMMDTNPEFRDKRSYMKNEHNLHDVLKKFGNNPILNAIILTRSNQVAMYCQPARYSEKGLGFEVRLRDLDAEPGRKEKEEMKRIEDFIVNTGKDKDVDRDSFQTFCKKIVRDTYIYDQVNFEKVFNKNNKTKLEKFIAVDPSTIFYATDKKGKIIKGGKRFVQVVDKRVVASFTSRELAMGIRNPRTELSSSGYGLSEVEIAMKEFIAYNNTESFNDRFFSHGGTTRGILQIRSDQQQSQHALENFKREWKSSLSGINGSWQIPVVMADDIKFVNMTPTANDMQFEKWLNYLINIISALYGIDPAEIGFPNRGGATGSKGGSTLNEADPGKKQQQSQNKGLQPLLRFIEDLVNRHIISEYGDKYTFQFVGGDTKSATDKLNILKLETQIFKTVNEAREEQGKKPIEGGDIILDASFLQGTAQLQQDKQYNDGKQKERLQMMMSLLEGDNDDSEEGQSTDSSNDDKEIGTDAQIKGDDNVYRTQTSNKGQGRKGEKSSDFKH

Entity 4 polymer

描述 description	Capsid protein
分子量 formula_weight	33757.3 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

MEKPYMIGANSNPNVINKSTTYTTTTQADEQDKPKYTTRLEFDTIDMIRFINDRGIKVLWEEAYFCPCLNPDTGHPRVDCPRCHGKGIAYLPPKETIMAIQSQEKGTNQLDIGILDTGTAIGTTQLEKRISYRDRFTVPEVLMPQQMIYFVNKDRIKKGIPLYYDVKEITYIATQDGTVYEEDYEIKNNRLYLNEKYENHTVTLKILMTLRYVVSDILKESRYQYTKFNQPKSKFENLPQKLLLKREDVIVLQDPYKVNDGIEEDLEIQVDDPKASASNPSNLGGFFGGAFK

Entity 5 polymer

描述 description	Baseplate hub assembly protein
分子量 formula_weight	31799.7 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

MAITSVDSYLLSEIKPRLNTVLENCYIIDEVLKDFDYQTRESFKEAFCGKNAQHEVTVGFNFPKFKNNYEAHYLIQLGQGQETKNSLGSIQSSYFEATGDTLVESSTAIREDDKLVFTVSKPIGELIKVEDIEFAKYDNLQVEGNKVSFKYQTNEDYENYNANIIFTEKKNDSKGLVKGFTVEEQVTVVGLSFNVDVARCLDAVLKMILISMRDSIEEQQTFQLQNLSFGDIAPIIEDGDSMIFGRPTIIKYTSSLDLDYTITQDINKLTFKERKDWK

Entity 6 polymer

描述 description	Putative non-cytoplasmic protein
分子量 formula_weight	10146.7 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,n

MSIEKKEEVIAHNEVVFRSLTQGLYVKEVDIYSDVVSYTKDVDEALAMPNTINFKNSRKYKKLIMNLDLEPLNKIQKVIYETHLEGL

Entity 7 polymer

描述 description	Non-cytoplasmic protein
分子量 formula_weight	17885.2 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	S,s

MADEISLNPIQDAKPIDDIVDIMTYLKNGKVLRVKQDNQGDILVRMSPGKHKFTEVSRDLDKESFYYKRHWVLYNVSVNSLITFDVYLDEEYSETTKVKYPKDTIVEYTREDQEKDVAMIKEILTDNNGNYFYALIGETMLFDENKLNKVKD

Entity 8 polymer

描述 description	Putative neck protein
分子量 formula_weight	34191.7 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

MVNSMFGGDLDPYEKSLNYEYPYHPSGNPKHIDVSEIDNLTLADYGWSPDAVKAYMFGIVVQNPDTGQPMGDEFYNHILERAVGKAERALDISILPDTQHEMRDYHETEFNSYMFVHAYRKPILQVENLQLQFNGRPIYKYPANWWKVEHLAGHVQLFPTALMQTGQSMSYDAVFNGYPQLAGVYPPSGATFAPQMIRLEYVSGMLPRKKAGRNKPWEMPPELEQLVIKYALKEIYQVWGNLIIGAGIANKTLEVDGITETIGTTQSAMYGGASAQILQINEDIKELLDGLRAYFGYNMIGL

Entity 9 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

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7. 引用文献 (1)

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分辨率 resolution	4.30 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	21731

fit	/app/data/saxs_computation/r6/8r69/8r69.fit
pddf	/app/data/pr_computation/r6/8r69/8r69.pr.out
profile	/app/data/saxs_computation/r6/8r69/8r69.dat

Neck and tail of phage 812 virion (composite)

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 non-polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)