8y6v

Near-atomic structure of icosahedrally averaged jumbo bacteriophage PhiKZ capsid

Method: ELECTRON MICROSCOPY D_max: 331.6 Å Quality: EXCELLENT

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	8y6v
沉积日期 deposition_date	2024-02-03
最后修订 last_revision	2024-08-14
结构标题 title	Near-atomic structure of icosahedrally averaged jumbo bacteriophage PhiKZ capsid
关键词 keywords	phiKZ, capsid protein, viral assembly, Pseudomonas aeruginosa, jumbo phage, 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	125.30 Å
零角强度 I(0) i0	52270200000.00
分子量 molecular_weight	1969800.0 kDa
排除体积 excluded_volume	2471600 Å³
包络体积 envelope_volume	4118600 Å³
水化壳体积 shell_volume	273880 Å³
包络直径 envelope_diameter	466.1 Å
壳层 Rg shell_rg	96.41 Å
包络 Rg envelope_rg	127.30 Å
形状 Rg shape_rg	125.30 Å
总 Rg total_rg	125.20 Å
总原子数 total_atoms	138685
残基数 n_residues	17716
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	331.6 Å
Rg (实空间) rg_real	117.50 Å
Rg 误差 (实空间) rg_real_error	1.52 Å
I(0) (实空间) i0_real	5.0130e+10
I(0) 误差 (实空间) i0_real_error	1.1160e+09
Rg (倒空间) rg_reciprocal	113.00 Å
I(0) (倒空间) i0_reciprocal	50130000000.0000
解质量估计 total_estimate	0.9193
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	110.5 Å
偏度 Skewness skewness	0.224
峰度 Kurtosis kurtosis	-0.746
角度范围 angular_range	— – 0.0600 Å⁻¹
当前正则化参数 α current_alpha	0.5836
最高正则化参数 α highest_alpha	777700000.0000
实空间数据点数 n_real_points	13
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.005; Oscil: 0.998; Stabil: 0.988; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; 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 (11)

Entity 1 polymer

描述 description	gp28
分子量 formula_weight	36511.9 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	D
原子数 atom_count	138685

MFLLPYETTVCKTLYNPTGGGKLYPKQYVDQIENAIKKANVYLPIPPVDARNGETLEHSGQITPVDDFEDIKKFTQIVNIGDRDNPKLVVDARLYKKIEQRTGIPRIIQQNEWQFQYIRMALNIKLLREGPDFLHRLGDIPVKVFYNWISGILTQKYSLPPESTQAIWVICAVYYFAMQDDDLTEPGQERDRLIPIISRLTYIPAGFIADVIDTLGPLHNAGDLAYEISTNGRSIRMGKLKFSDLQLLVSPSWFGTASRENVGVALEHMPTYITLIYMALADRSYRKTVLSQKVEMISRSDDASRFINLVNEAVSSQFVK

Entity 2 polymer

描述 description	gp35
分子量 formula_weight	29713.8 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	B

MAKRKARAVSAPVTLSEISEIPNEVTNAEDSVNELETTPTEIVSTESSENENTTADSENTAATDSTTDEESEDTSSTEANGDGESEEPDLSENQEDPKEPIETPEEPVEDDDGSGDPDGGTSEEKPTEGDPEDPEEPTEPTDPEEPTDPVDPVEPPPEEPKAFQLNLATVKSQFGDLPTYWAIELIKRYFSAPPAIYIPDVVDNPDFKIMVQQVKFFGNGLRPIYNSKNMITFTTMLEGASEATILEDMKKQQPALLSLLPWYDPNAEIDK

Entity 3 polymer

描述 description	gp85
分子量 formula_weight	16438.8 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	E,F

MQQLGFELSRILKQLPNLGGSDRKTRAMLLANAVALQIPFETLLDFDEQQDKAVAKFKKILSKVNENIAVDTKLAVTYFNNILRIRQSLITGITDPCLVKAVLTSDTANDYLTVDDVNIVSAVVNGPDYNRIQADMGNALNQLIGSIDE

Entity 4 polymer

描述 description	gp86
分子量 formula_weight	48893.8 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

MSEVKPMSHVKEVDVEEEKLFFDENQPEMVEGEEETVSSASAPEVLAKMCVAVEAIHQLSDIYAITKLEGVSKPDVDGIRALVKRMSTEGFEAPKKAVASLEQYASMFTPTRSTLNVTISQEAVMATIINTLKTWFEKLMELFAKLIRWISDFKKRDVVVATRYGKIVRAVDQARTLFQELLVKNRLGNRKDALLEKFDAIAQSIIDDPKILASRIYAAAFGSVYYQKEIININNEARTELGTMEKLVGTIIEYVNYNGDDYRALMPIANIREIGKLATRCNELSTVYPDRSSIPDFPDKNFWKNSHLLKDRFVAPLDDLLKAYRNSSDALRKLKQLSRNYSQETIDAIGESVQLINTSLEGMRRITDTMFEYSQAQYLAASCVLNYYGKCAQVVSEDYKIHGFNDAIREWQRRFDKVIDDFKRGYAM

Entity 5 polymer

描述 description	gp91
分子量 formula_weight	20817.6 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	H

MEGIDMPATNAVRPFGRNYSGGQQQAISRFTARPGDPQVEELYLIFTNFPAQTAYWEFHKKVLACAIRLFSGNYNWFILQDNNSNIDSYNYQFLLDTVRYIATGHRRISITQWPMLLATEPDAGAQLIEPRAEIATLFNELKLDLDTVSMIQNWVKHKNGMNDLMYTLHLLFGSVEVIDKD

Entity 6 polymer

描述 description	gp93
分子量 formula_weight	47656.1 kDa
来源方法 src_method	nat
拷贝数 entity_count	3

聚合体 Polymer

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

MSLLKMLDKLSLESIEDQGTTIHGDVELVVENETSADVSSVLAEVDQIENNPVEEVLDADDAVQPTALDTEVTIVQAEDELGLIEDAKEALEKFQGLLLQAGEDGISRQAAAFMHVGMESIDRILGIEKSGLTAALENYDASPRSAIQKAAVISLEDLKEKLKEAGKKALEIIKKIVAMIKQKIKDFNPKLIALDMRITKTIDAIKSLKAGDLKKEEIKFTPSEYMVSSSGFIANNPKTIADFMTVFSTQYVSALRKYGELGVRYLKGDKSIDIDQVTSDLQAKMAEDINKAVEKAPGNVKLEVTSSKSGVNKWEVVEGDGETDLHEVEVDVRAPSKILAHLNILKGLVIKLQDFNKIDYKIAENLEKALADWNPDEAGMSKETARDALNIGGIDNSALVNYIAKCIAAQYTFIVKHELAAYGKETSKAPENDEK

Entity 7 polymer

描述 description	gp119
分子量 formula_weight	20254.0 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	J

MTQVLVMPKAVFESYKTAGVQFNKLLDTNYIVSETSVNDLAEIHQALTAFPFLLPEKLDIKLAVSPIIKVAELGEIDGPEQFKMKDLHNRLESRLATNELRDAGNRNLVYDYYLYPVDENLWVAVQQSAHIASSDPRRVSIQLNHTFFDSMINEMLNTRPRESVASTQIFTYYLESC

Entity 8 polymer

描述 description	gp120
分子量 formula_weight	83022.9 kDa
来源方法 src_method	nat
拷贝数 entity_count	27

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,p,q,r,s,t,u,v,w,x,y,z,A

MSVHALRELFKHKGEKNYEVFSMEDFIGRLESEIGLNDSVVSQGRSLISSISHENFGTVQATDIQDAAAIYNKMQMLVNDYGFERVSSSDPQVRAREERVRENQITAATMAAIACADETKYIRALRGITKAKASNEDHVKVVQHQFNGPAGGIQVFENGVGLENYNEKSQRDFRVVTIGYNLAASRQDEFAERIYPTTVINPIEGGVVQVLPYIAVMKDVYHEVSGVKMDNEEVNMVEAYRDPSILDDESIALIPALDPAGSNADFFVDPALVPPYTIKNEQNLTITTAPLKANVRLDLMGNSNANLLIQRGMLEVSDTIDPAGRLKNLFVLLGGKVVKFKVDRLPRAVFQPDLVGDTRNAVIRFDSDDLVVSGDTTFIDGSADGVINDLKTAKLSLRLSVGFGGTISLSKGDSKFGATDTYVDKVLNEDGQVMDNADPAVKAILDQLTDLAVIGFELDTRFTNTNRRQRGHLLQTRALQFRHPIPMHAPVTLPMDTMTDEGPGEVVKALTVNTNIRNSNNAVKRMLNYLAQLREVVHNGYNRPKFGIIEGALSAVMRPTYRYKELDLEKVIDTIKSKDRWDDVCAAILNCVKAELFPAHRDSNIEAAFRVISGNQDETPMYLFCSDKEIANYLMTKGDDRTLGAYLKYDIVSTNNQLFDGKLVVIPTRAVQQENDILSWGQFFYVSTVIADLPITRGGHQVTREIAAIPFNLHVNNIPFALEFKITGFQKVMGETQFNGKLADLKP

Entity 9 polymer

描述 description	gp162
分子量 formula_weight	57705.1 kDa
来源方法 src_method	nat
拷贝数 entity_count	3

聚合体 Polymer

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

MAKKKTVPAMDFFASLERVSDAEDKNVNLDVGKELPEQLKDDEDGKVNPCDEVTNVVTNTPIDVCKGPDVDGTADKINDKKIHVSQGLKEFQVAKGDRVENEITETADEMITKVSDTKDLNVSTKKPHQIADVPSNEDISIMEANETEQLDHGYDATALLETTEDIITGELDDHLESLSVEMFTIVNELTKVESVQTALENYIGLVSNRHHRGHDVDHDLAKAISIALESFDYKYFNNTVPSMESFISPLTRPKASIEVLDNLQAKAKEVSTVALDFIKKLIRIVVETYQRIRQNVSNQIERVNKIMKRVKENELPDEVRTIAIPRDLILGDTGESWVGVDPVQGVTVIRNLFDSIEKNGLRALKAALAGKTTDDKALALAKGMFGTATKINANGVRYASPVVPGNRVYTFGKDKAAVDFSILDAPGKPNYGITVELLVDKNVVMAQLKAVHNLLNHLNNIRGISKESTAEIIAQMTDKEATNVGKAYLTGTTEASNDLFKCVMIWITVLEKLVDSEIKETE

Entity 10 polymer

描述 description	gp184
分子量 formula_weight	25300.8 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	I

MSKPNLEWLASLESKEAKSTVDSSDMDNDQKEGSDKSQQDEATEPEKKITATDVQIAIEEYARIRALTTTKDLPTDPEPGDTYHVNGVDWIYQEDGGWVTMQGIYGHEHFDENGLNIEASGIDQKSGATKRYVVTGYNAQTNPAAMPGDNLTECVILMQNGLVPEVGVNGLTADCLLKIVKDLFEGYQAGPFACEENQVVINSMDRALSAIHQRLVRRKEQGTEGTYSGN

Entity 11 polymer

描述 description	gp244
分子量 formula_weight	13427.2 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	C

MPTYIELINIVNDDTPEDDAVISDLMSQMNDKQTVLDSCRINHKGNAYFKFHVKGSISKDKLKALNETLKDSNLVVTDASTQRGFMPPNKFDDITYTEESVGYRAMVWTSFTIEKLLV

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7. 引用文献 (1)

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分辨率 resolution	3.50 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	903900

fit	/app/data/saxs_computation/y6/8y6v/8y6v.fit
pddf	/app/data/pr_computation/y6/8y6v/8y6v.pr.out
profile	/app/data/saxs_computation/y6/8y6v/8y6v.dat

Near-atomic structure of icosahedrally averaged jumbo bacteriophage PhiKZ capsid

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 (11)

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

Entity 10 polymer

聚合体 Polymer

Entity 11 polymer

聚合体 Polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)