SAXSdb — 8zdo

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8zdo
沉积日期 deposition_date	2024-05-02
结构标题 title	Cryo-EM structure of Mycobacteriophage Douge baseplate (gp13, gp17, gp23, gp16, gp18 and gp20)
关键词 keywords	Mycobacteriophage, phage structure, Icosahedral, cryo-EM, protein assembly, VIRUS, VIRAL PROTEIN; VIRAL PROTEIN
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	72.37 Å
回转半径 Rg (电子) rg_electron	72.07 Å
零角强度 I(0) i0	20236900000.00
分子量 molecular_weight	1230300.0 kDa
排除体积 excluded_volume	1544400 Å³
包络体积 envelope_volume	2224500 Å³
水化壳体积 shell_volume	243890 Å³
包络直径 envelope_diameter	297.1 Å
壳层 Rg shell_rg	81.72 Å
包络 Rg envelope_rg	71.40 Å
形状 Rg shape_rg	72.04 Å
总 Rg total_rg	72.25 Å
总原子数 total_atoms	86910
残基数 n_residues	11289
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	268.8 Å
Rg (实空间) rg_real	75.59 Å
Rg 误差 (实空间) rg_real_error	1.86 Å
I(0) (实空间) i0_real	2.0260e+10
I(0) 误差 (实空间) i0_real_error	4.3390e+08
Rg (倒空间) rg_reciprocal	72.80 Å
I(0) (倒空间) i0_reciprocal	20260000000.0000
解质量估计 total_estimate	0.8686
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	85.5 Å
偏度 Skewness skewness	0.642
峰度 Kurtosis kurtosis	0.660
角度范围 angular_range	— – 0.1100 Å⁻¹
当前正则化参数 α current_alpha	0.9522
最高正则化参数 α highest_alpha	2770000000.0000
实空间数据点数 n_real_points	23
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.610; Stabil: 0.888; Sysdev: 1.000; Positv: 1.000; Valcen: 0.935; Smooth: 0.881

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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 (6)

Entity 1 polymer

描述 description	Tail tube protein (gp13)
分子量 formula_weight	32112.0 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,M,N,O,P,Q,R
原子数 atom_count	86910

MTDFYTIKDAQADLAIAPLNLTVLLAPYSTTPATTLESPTDGSLAIPPGYKSVGHFEKQAGLTLGNEFDSKDIEAYGEPEPIRTIINKRTTTFDFAMYQNQRNVLELIWTQDFSNIQPSEFGGIVLEAPKVPKNIYYRAILVGMDDRNDRPIWLYWLMPKVKLDKLDNQTLNDDNVIEYKPTLKAFRDDVVGYSVAQGFAGPGWRDLVATAGFGEALTALTITPGSPTVTVATGASHTAQLLVEGDNGINYTPDVVFTSSAPDKASVSAAGLVTGVAAGSATITATKGALTATATVTVTA

Entity 2 polymer

描述 description	Tape measure protein (gp16)
分子量 formula_weight	176109.2 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	S,T,U

MAEFVAAQASVLIVPTLGKGANSFHQKLKEQLQTVRESVDVKIKADTAAMVAEVQATKEMLERDPINIRVETDNNGIKELVKSVTEVRHKYEDLKGDFRRGLTLNLKVVGLSALSQLGPMLASLNTSIVQLSQSSLLLPGIMSGVASSVGAAVVGSRGLTDAFKAQSDASKNVAEAGKQQRDANRAIRDSTRDLNNAIRDAKRNIEDLNAQLRDAPLDEAEAMLNLQEAQYEASQKWGKTAFQQQRDALGLAKAESQLAETRRRNVRLGQDVAEANAKGVNGNDAVVAAQERLTKALEDLAMQTGPIRALNDAMAKLSPNARDFVDQVSSLKGAWDGLRSTVQDRLFDGLGASVQTLAGQDLPILERGLAGIAGAINGNLKTAMSQLATDENKGFLGRIFGNTEEAQNRFSTALKPLLDSFMQLSAVGSDYLPRLSNAFGDVLNRFDGFIERADADGSLDKWINNGLDAMTQLGNSLINVGSIMNTISEAFTGTGGKGLLELLETGTKRLADFLKGAEGQQKLKQFFLDARTELNNWKPLLSQLPGLIKNVATAGQQWANLVLPFLTSAASLLKEHPGLVTAIFTAYMTWRTISPIIGTINLLLSSETGMVGAAKKAGRAVGKGEGLTGKLGVLAGMVGQGGVVMTGLSLVAGFLINEWVTAQNEAAEAVSYHASMISRLKGEMDGLTGSLTTQGLQGKLDAARQWTDIHQTDGKPKDLVAAANSFGVDLPTFMGALTPTNQAARNAVTGKARQTVLDDLNKQGLETVLGKDALNALNLYNQNAAPDKKITNDVLADIATGVNPESKKLFEDAKKSNLIHFNESDLLYGYNKPWGFIPGTDPSGKGLSPVARDAANVSGFVLNDTGNALQVGSDIRSTNEALYGKAVLTPAGQQMFGQFGSPQASFENGSKDAAVRVDTTLQNLPPQFVKDVESNGGHFEELPDGVIIHMRKDRAAQYVTAGSYAGGGFLSGPGTGRSDSMLARVSNGEFITRAASVAKYGRGLFDALNSGTLDPSMLPRFDSGGLVDIFLPGGGTAAPPPTGSANPVDLARGLPRGPAVQSAPANRFDPSPLPTDLLPKPVIPMPDLANPGLYDPATGKYGAAPASAVQQPLKPGVDGDKGETSGPNVPPTDPRSPGYKQPNHGLGGSPGPGNGTPHLTGPGGTPVSPGAASALPSNGGIPGLTPSATDPLGLSGLPKEIQPVTILEQIGEILLSAVLGFFGLDPTYFNIGKRIFTGIKGDKPNEANPGVQSILDGYKNPLADGQNPYVGTSIYDASFDPASQRASNMAELMRGKPYTWGGSSLDGTDCSGLVMYVVDAYEGKEFSGRTGGTGGFASSLPAKGGVIISDPSQAPPGTLRVGWNASHTAGTLPDGRNFESSTFGKPIAVGAGASGYNDPQFTNWAYFPAPGYANGGFLSGAGTGRSDSMLARVSNGEFITRASSVAKYGRSLFDALNAGTVDPGMLPGFADGTPPIPGLPVPQPQTPQQAGPLPDPNGQDAQAAQQVTDTAASALDGVAGAMNGVNMGSSGAIPGADAPDGAQQGKDPRSILGAAPTNTDHNNPALSKGIQGAFSTVGSLASMAASAAMSAGTMGAGAAGASGAAGSGIQAGAQIAGQVATGALNILSSLLVGSAPGSTGTTQSAYGAPVLPQGPPQSSGGGPAVVNNYGDIHTANYDEFYKGQQRREAQQQAPILPVR

Entity 3 polymer

描述 description	Baseplate upper protein (gp23)
分子量 formula_weight	33673.9 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	a,b,c,d,e,f,g,h,i,j,k,l

MLSTGPIMETLTLTVGSAFEIPGWKLRGEYPAGTTSHLVFTDAAGGTLGEFEGTVSAKEIHYLQAPDDVKNIPHGANFQLFVTYPSMQPQCLYFGTAIRKEPRYPLSTVVSPEDSAVQYKANFVGQYIGPMWKPMGNGWGSLGIHTHALISEAPSMGPNYSLFSSAAARWLWSMNMDSVTIVVRVLNVGAGKFNVIVCADYQMQTYLGIQFETGISNNKVHVITGDGPLNWGYQGDAVNNTTANGDVYTIKYNDLLDTISCYKGTSLTPLIEASGLDVPHGEGFRYTGLAWNTALLSPGVEPTAWEAKDGV

Entity 4 polymer

描述 description	Distal tail protein (gp17)
分子量 formula_weight	33772.0 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	m,n,o,p,q,r

MTDFLKIELIGRDGSHWVLSGPGMGQQGVTLNPNLQQFYDAPVKTLYVPGPFGEEYAGKRVQRREIVFSVQAYDEDPDTWSTVDSLWRWAWDYDEESELRVSTSDGTRFLKVRLMEEPKPYYEKDPHITADNPIVMTVTATFPYWQDEPEELIWTTLSTEDMTRFPVRNDGDVPVWLKWTLTAPGLWILPDFSWGNDMYSRGREDLGRTVAMPELVAGEHVSVDSDPRVQTLIAVNGMPTQNRWKGNDLLYPLMPGKGAEIPVQLKNAPEGGACKLTRPRWYSRPWSRPGVRLNG

Entity 5 polymer

描述 description	Baseplate hub protein (gp18)
分子量 formula_weight	65026.3 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	s,t,u

MANNWTDILAASDGDEWAAFKTIEAQADEVRAGHQALRRAKPLIRLWMNNPDGSEGLVYVGRVDYDDTIRGSFPFKNNTPSQGVLELRDDNYLAVWLKQLPNNPELKKNVVITVDFYGGKKRWSGLLDKWTIKSKEHVKYLEVTFNDDLTMLQYLLCPPNPALPIPVLQFPRIFGIAGPAKWAISTLIFINLFRVQGNLWTLPDDPFNLESWDDILDWSDWQCFVKSNSFLLDDSSVWTFLSSRMNPVDSIIADALDDAQLTITYRRVLTDDGETAEGFPGAHGIKNGALVFEIVDNSNATALEGTFFSGTIVDGFARSVLLYGGGFVEDTLSVVSDDQTLQPDEYYQSGWLATMAKMPWLVVRDNEWTPIESSDLSWGPAKNVSVIVGGDNPAADAIAKLIIETTGNLLGYFLLGGFSSAGTIAADIIMPFLVGTIAAWLQWKNTGRATELGWVHYWELYQQGAETNSWSLAALAALRGGFLVGRSETVHLMALHDSWIIPGLHIDIGQRMGSTVNSKGVENIVWVNQLEEMTAAWDNSAGQTMPLSWVLKAGKSDRAMSIGERVARLAKKMSEALNNVGVHIVQS

Entity 6 polymer

描述 description	Central fiber protein (gp20)
分子量 formula_weight	92774.4 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	v,w,x

MTMPNGSGGLDPGAWLSHWVNQADLSSLAGRTEDEVRAYFENLVQADSGWGDASNTFFNLILGGFQNLSEFVTLIVQAVTGAPGGLTDLQAFLTERWGDLADAFQAVANLIDAIAGEVGSSLADAIAKLATFLTELSPLNAGMLFGLIGTNHLPLLSVSHIANINPELLVNAGFDSDVSVVDNPYWDWDGTVGRTAPLGAVKVVADGTIKDLLSGPDAIPVVEGQKLNVSAWLKYSGLVAGAGAGSIRLSGTAYSADGEVVAYPDFGGIPDGASGTSDWTQVTGQYVVPAGVTQFRLRLSVRENATGGTVWFDDCSVKKAGLLPQGLVDGLVQALSDLLTWLESLVDNVLSALGLDPIGTIVDKILDLADEFGDWLGATEDTAANLSNLLTKLLSDPASVIGPLAQSMITGLTGALGNLNTAINQIGDVLVGTVVTPINSAISNVIDWFNSLLNFQDTTTSNQINQQNFQIATLASGIKKQQWECRYSTAFVTFPEMFCDWGFALGGTTGAQSTGTAHTHTLNTDGLAALQIQILPAGYAIGGYIGISDTTIVDTIAMKMYKETSSAINNVYLEVFREDSTGALTSVGSVDVSGQLTTASDYVEATLPAGVIVNAGERYVVRMRNATTVGNRVGVSVMKELVGGRELSIRTETATDSNKTFYTPSEVLTAQGVSVIMPWAMMAAKNLATTDQSFSDDFNRSAMGGLWFLKSDTGTNQVGVSGGRAAFSGLTDGNQNALYIRPTAGDKQWVEATLYETGIAASGAREGLLMHANRDLSQVVYLGVNLNTAKIYTGPWNSLTERASVSTTGNDVLWQMYFDPATAAYTVLKNGQASGLTWTDSGSVVAHGPNYRFGGLRISRATFFNAGRIDNWTLKDWA

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7. 引用文献 (1)

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分辨率 resolution	2.97 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	78927

fit	/app/data/saxs_computation/zd/8zdo/8zdo.fit
pddf	/app/data/pr_computation/zd/8zdo/8zdo.pr.out
profile	/app/data/saxs_computation/zd/8zdo/8zdo.dat

Cryo-EM structure of Mycobacteriophage Douge baseplate (gp13, gp17, gp23, gp16, gp18 and gp20)

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 (6)

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

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)