SAXSdb — 8vjh

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8vjh
沉积日期 deposition_date	2024-01-06
最后修订 last_revision	2024-10-02
结构标题 title	Cryo-EM of tail-tip of bacteriophage Chi
关键词 keywords	Flagellotropic bacteriophage, Siphophage, Tail-tip, 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	63.52 Å
回转半径 Rg (电子) rg_electron	61.29 Å
零角强度 I(0) i0	848737000.00
分子量 molecular_weight	226520.0 kDa
排除体积 excluded_volume	276470 Å³
包络体积 envelope_volume	485340 Å³
水化壳体积 shell_volume	72225 Å³
包络直径 envelope_diameter	244.1 Å
壳层 Rg shell_rg	53.26 Å
包络 Rg envelope_rg	65.01 Å
形状 Rg shape_rg	61.61 Å
总 Rg total_rg	60.02 Å
总原子数 total_atoms	15967
残基数 n_residues	2219
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	211.0 Å
Rg (实空间) rg_real	64.59 Å
Rg 误差 (实空间) rg_real_error	1.78 Å
I(0) (实空间) i0_real	8.4710e+08
I(0) 误差 (实空间) i0_real_error	1.6100e+07
Rg (倒空间) rg_reciprocal	62.26 Å
I(0) (倒空间) i0_reciprocal	844800000.0000
解质量估计 total_estimate	0.7973
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	3
主峰位置 r_peak_primary	59.1 Å
偏度 Skewness skewness	0.720
峰度 Kurtosis kurtosis	-0.036
角度范围 angular_range	— – 0.1250 Å⁻¹
当前正则化参数 α current_alpha	0.0038
最高正则化参数 α highest_alpha	41160000.0000
实空间数据点数 n_real_points	26
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.735; Stabil: 0.996; Sysdev: 1.000; Positv: 1.000; Valcen: 0.880; Smooth: 0.286

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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 (7)

Entity 1 polymer

描述 description	Minor tail protein
分子量 formula_weight	143342.5 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	A
原子数 atom_count	15967

MGSKSKKVTVGYKYYMGLFMGLFRGPVNEITEIRVGDRTAWTGSITGNTTIQINKESLFGGTKAEGGIDGPLEVYMGAPTQTVSQKLKNMLGGRQPEFRGVVTAYFDGLICAMNPYPKQWKFKARRSTAGWTGGVWYPEKCLVKMQGYDGQGNQHEIHAMNPAHILYECQSNYEWGRGLSRTLIDDTTFRLAADTLFNENFGLCIRWNRQDTLESFMQLILDHIGGAMYVSKVTGKLSLRLIRKDYDFDTLPIFDTDSGLLSIQEATNASPANLVNEVVVTYHNPVMDEDQQVRSHNLAQIQNQGCLNSNTIEYLGIPTGKLAMQVAQRDLRAASTNVRRFTVICDRRAWNVQPGDVLKVRDPKQRGLTEVVIRVGTVEDGTLPDGKIKVVALQDQFAFQLNTFNQVEPPAGYEPNLTPAIARRIVYEMPYVDLVQQLPDGELNAVGPNDAFINSQAEKPTDMSAAYDMGIMAEGESGFDVRGNGDFGAFGSLASDIDYLSTQIVLSEMTDMWDDVQPGFVARIAKPVLDGQRTQMEIAEEFVRIDAINGNVITVARGVLDTIPFRHQKSEMLWVTTYDGGTDWQKYAGNESIDIKILPWTLGGGRFPIEDAPIDHLDMDFRQIRPYPPGNVQHYLASTSTLQRWYVPSALTYTANAGETPDTYTLTWAHRDRVLQGDKPVPHIDGDIGPEPGTSYTIRVYNQEGTLVRTESGINGTTWNWPYATAAADMNVEASLFDPVLATLRLTSARNGRESWEYYEMKVSVYKKPPQFVYDASLMQFAAQPYNATSDPNPPTPPMDGPYVSSLMQFAAQPDGSEDFGPAESMNGPNVALLPHQVTQTSSIITPLDTLLYETPYIQLSRDGRDLNTSKVSAYVARSSDRTVDSYTLFTKHETDANYTSSGTQPWTPWGMSTVGLGFFTDEVTIDPTSDKDGVPVAPAKVGDLLLIDQELVSITAINGRTYKIGRGVADTIPAQHYSSRPVWLISVGFGYSDMAFGDNEKAMVIIRPDTYGTDIPLSKLYPLQLQMQYRPKRPYPPGLMMIGGQPFFNTASGLADDFNPYDNLKAKDVVCTYAHRNRVSQSTTARDHFAVGITPEPGVKYRVRIGYAYWSQSGSGFSLLSQFETEDAGFIMRAADLERWGRQAGYAQDAGGYSTLNVTVNAIRDGMLNWQGYTMTVRVPSFPLPPGQKPGGGDGPWNPPGGGNTGGTTPPTEPPDRPDPSEPGTTDPSEPTKPDEPEEPQPPVDPEDPDTDPPEPPEPPVDPTNVPGWSLSWDHGWAMTLPDFRYVPPADEEPE

Entity 2 polymer

描述 description	Distal tail protein
分子量 formula_weight	63032.6 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	B

MALSGLRPAREQFNQAIYDALNGAYQLYVQDAFGQAAANQTYYMAKWMKLKAGTYTAVMYVDDSGTLSIDHAVVATAAIGTNPNSGEFTVAADGVYRFDCIYSNVPADTPAYMAYQLIRDGQTVEVSRANDFIADIVPIPDKALGPKPPYSDDVRLTYPVFLPLPNWKDGVTERIEWQTDVMISESGAEQRRPIRLHPRRSFEATFLRWEENRTLLDTTIAGVGQSPLLLPLWHDMTATENNAPAGSVDIFGQFRVKDFNVGDVVMFNRGTTWDYETNIIAGLDIDAGHMTLTFGLQSDTPKGTRLYPVRVAQIREAMNGQQMTDSVSQTQVRFFCTENYDLTPSWSDFPIYTRTGLHIFVLPEDWGSSNEITSDRLTYNFDNQSGPVVVVDPGGQNYGTVKKSYTIKGRTADRQFRQILFALRGRTKTFHLPLDTNDFILSRDINPADGALVVRRCGYTQYIGGTQETKRDIMVELYDGTRIPTTIISSRIVGDEEWLFLSQSIPATSRNDVRRIGYIPVARLDVDGIEIKRLTDSAGVSQVSLTFKFFDDRRIATPLPLS

Entity 3 polymer

描述 description	Baseplate hub 1 protein, gp27
分子量 formula_weight	29348.9 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

MSYNIIETSNDNGRPVFMYEFRLLDKYWRYTSADAKVSALGSIWEPMGVSDDGIKQTGEAKTDALNLTLPNSNPVVGLFIGTPPGSPVTLTIRRMHLDDNDPVVCYVGTVDSINQGENPTVATVTCSTLSATMDRNGLRLSWSRGCPHALYDGQCRVNKEAFRVDATILTVGAGTVTAAAYATRPDGYFAGGFIEWIDPVYGVERRGIETHTGNTITIFGTVDGLAGGYILKTYPGCPRTSAACDTIFNNLANFGGIPSLPDRSPFDGNPIF

Entity 4 polymer

描述 description	Tail Tube
分子量 formula_weight	40375.4 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,K

MNDNYQNNYVVGRGTVYFDRFQDGTNRKTGEMYFGNTPEFTINTDSETLDHYSSDHGMRVMDASVLLEASQGGTFTCDNINADNLALWFLGEVSNTTQTQQTDAKEVFNPIMRGRYYQLGTTDDNPTGVRGVTNFQMVKADASIAISVGSGDITSIVGATVVNPAGNYEIDLEAGRIYIEPDSTDLSGNVQIAVQYDVDAQKRTLVIGKSNMVYGALRMISDNPVGLNKNYYFPKVSIAPDGDYALKGDDWQVMSFTFKAMQLNNITQRVYIDIVEAAAAVDPTAQRTIEITPASTTATTGGAGVVCTVTVRDGTGTAVQGDAVTFTTVAGATVTPNSATTGATGTATTTVNRAAAGTATVTATLANGKAATTGTITFSAP

Entity 5 polymer

描述 description	Tape measure
分子量 formula_weight	153960.5 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	Q

MANSKDVELRIRARDYSQKPLKAVTSAIEQMAKAQDEQRKAAERGEISTRDLEAAYKKLESAGSQLLKLNSLIEVFKRQNQAMTEATAKTEGLRQKQADLQKTYDSTEKVTQKQERALARVTRQVEAATRAEANQAERVNRATRDLERYGIETSKVGAAQAGIVTSVAQVNRVLERQDEIISTSAAAAAQAKVIRGLQQQADQAMATARGYQTLGRVVQQATGQLGPLGTQIQTIVSPAEAARRTLSGLENQVHGVTAELARNSKEVENVAQKVRMLNEANKTVSALAQQIDLYRQQVATLRNARTEYQQARQDVIKLAQQMRTATTDTGALGIQMQAAQQRLSAAATAMRNTATAARSTQAALRAAQVDTRNLSDAEARLISTSQQSAAALNTLSTATNRNSQAARDGSKAWSLFRDEGRTTLSFLQRIRGEVLALTTTYVGFQGAISLAGGAIDAYKNRQQAMVKIANVVGNSQAAINKEWEYMVGLANTLGIDITTLSQSYTKFAVSAKAVGLSLQDSKFIFESVAKAGRVFHLSQDDMEGVFRALEQMLSKGQVYAEELRGQLGERLPAAFALFAKGMDMTTAELMKAMENGEVTGEAVINFAREQAKAIDAQLATAQKGVDAMEARARNAMNAFQLALADAGFIEAYVQMLNKITDFLNSEDGRAAAVKLGEAFGMLADAVTWCIENVDTLITALSILAGLKVVQFIGGMISGLKNLLPLFNTLSKIGAGIITVLEGVAARMIAAEGAIGLLGVALKGLTRLIPIVGWALLAYDIGAIMYDQSQTFREAVNAVIRDFKNLGNQLAAVVDTIPALLYDLAVSVLRPITTMFADTTQAIIKWIADVLKLIPGVGQGLSEWATSIGDDLTKEQRGFLESTGRIWDNVNKQWVKLNDDMVAKNADATDKIRGQVNQLAADMAAITKGEGFQFTQDPGTGVTKRSREIAGLTKELNKMEEAAKKADVASRKAEQRKNLSGRLAIIDEEFAPQYARAKSIGGSEGDALTKRLDAVVAARKKAETTLFNSQQRTTGGIKKQENALQALINKYNELNAAVGVKEVKIDPNATFDDRLAAKLAAVNTQYDQLIAKSKKLGTGGENLAGQFEDLRKRNLEYATTQAKLEELKRIQDQLNAQQETRKNLLDEINAKRQAGIISEDEAVSQTVALYQNMNAGIASSAEQLDVFAQKIKDTMSPEEFSRIMAQIAAVKAGLVDVTGTFTTMDTTVVQGVLDGMSTALSSIVDEMALVVAGSQSIGDAFSNLGVAVARFFADFLQKIAMAILQQMALNALASMGGGIGSAAVALGGTVAKHNGGTVGSKTTGGTQMKGGISPAMFANAPRFHDGGLPGLRSDEVPTILQKGEQVLSKDDPNNVLNQSRGGGQTAQSPQGLRFVLVDDRSKVPEAMNTPEGEKAVMQILQRNVPTLKNLVG

Entity 6 polymer

描述 description	Tail assembly protein 1
分子量 formula_weight	8278.7 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	U

MWWALAMLVASVLINAALAPKPASAKPATIQDFDIPQVKEGTPQSVVFGEVWTADWQVLGFGNFRTKAVKAKQAKK

Entity 7 non-polymer

描述 description	FE (III) ION
分子量 formula_weight	55.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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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	4.20 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	2159

fit	/app/data/saxs_computation/vj/8vjh/8vjh.fit
pddf	/app/data/pr_computation/vj/8vjh/8vjh.pr.out
profile	/app/data/saxs_computation/vj/8vjh/8vjh.dat

Cryo-EM of tail-tip of bacteriophage Chi

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 (7)

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 non-polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)