SAXSdb — 8hqo

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8hqo
沉积日期 deposition_date	2022-12-13
结构标题 title	Neck of DT57C bacteriophage in the full state
关键词 keywords	Neck, Portal, T5, 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	58.38 Å
回转半径 Rg (电子) rg_electron	59.13 Å
零角强度 I(0) i0	1163880000.00
分子量 molecular_weight	287950.0 kDa
排除体积 excluded_volume	361830 Å³
包络体积 envelope_volume	555600 Å³
水化壳体积 shell_volume	82241 Å³
包络直径 envelope_diameter	276.8 Å
壳层 Rg shell_rg	54.68 Å
包络 Rg envelope_rg	64.39 Å
形状 Rg shape_rg	59.09 Å
总 Rg total_rg	59.15 Å
总原子数 total_atoms	20871
残基数 n_residues	2552
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	222.0 Å
Rg (实空间) rg_real	58.61 Å
Rg 误差 (实空间) rg_real_error	2.35 Å
I(0) (实空间) i0_real	1.1600e+09
I(0) 误差 (实空间) i0_real_error	2.6870e+07
Rg (倒空间) rg_reciprocal	57.50 Å
I(0) (倒空间) i0_reciprocal	1160000000.0000
解质量估计 total_estimate	0.7612
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	49.3 Å
偏度 Skewness skewness	0.675
峰度 Kurtosis kurtosis	0.119
角度范围 angular_range	— – 0.1350 Å⁻¹
当前正则化参数 α current_alpha	0.0553
最高正则化参数 α highest_alpha	146800000.0000
实空间数据点数 n_real_points	28
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.490; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.488; Smooth: 0.929

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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 (4)

Entity 1 polymer

描述 description	Portal protein
分子量 formula_weight	45408.6 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	D,E,B,C
原子数 atom_count	20871

MGFKSWITEKLNPGQRIIRDMEPVSHRTNRKPFTTGQAYSKIEILNRTANMVIDSAAECSYTVGDKYNIVTYANGVKTKTLDTLLNVRPNPFMDISTFRRLVVTDLLFEGCAYIYWDGTSLYHVPAALMQVEADANKFIKKFIFNNQINYRVDEIIFIKDNSYVCGTNSQISGQSRVATVIDSLEKRSKMLNFKEKFLDNGTVIGLILETDEILNKKLRERKQEELQLDYNPSTGQSSVLILDGGMKAKPYSQISSFKDLDFKEDIAGFNKSICLAFGVPQVLIDGGNNANIRPNIELFYYMTIIPMLNKLTSSLTFFFGYKITPNTKEVAALTPDKEAEAKHLTSLVNNGIMTGNEARLELNLEPLDDEQMNRIRIPANVAGSATGVSGQEGGRPQGSTEGDKE

Entity 2 polymer

描述 description	Head completion protein
分子量 formula_weight	19203.9 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	R,S,P,Q

MQIITAEDYRLYGGLKRPELESGVEMMITAANALITSLLGMDDADAVDQLINTKPTRKKYFLSSPSATSVTKMTINDKEIDPEQYKLYSDGVILLKFSPPEGYMDVEYTQGGFNPIPEDLKLAACMLVDHWHKQDYRQAKTIGGETVTFNNTKSGIPEHIRTIIEVYRRV

Entity 3 polymer

描述 description	Tail terminator protein
分子量 formula_weight	18317.5 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

MDHRTSIAQALVDRIAQQMDGSQPDEYFNNLYGNVSRQTYKFEEIREFPYVAVHIGTETGQYLPSGQQWMFLELPILVYDKEKTDIQEQLEKLVADIKTVIDTGGNLEYTVSKPNGSTFPCEATDMSITSVSTDEGLLAPYGLAEINVTVRYQPPRRSLRR

Entity 4 polymer

描述 description	Tape measure protein
分子量 formula_weight	132626.4 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	x

MTDKLIRELLIDVKQKGATRTAKSIENVSDALENAAAASELTNEQLGKMPKTLYSIERAADRAAKSLTKMQASRGMAGITKSIDSIGAKLDDLSIAMIEVADKLEAGFDGVSRSVKVMGNDVAAATEKVQDRLYDTNRVLGGTARGFNDTAGAAGRASRAIGNTSGSARGATRDFAAMAKVGGGLPLLYAAIASNIFVLQSAFEQLKLGDQLNRLEEFGVIVGTQTGTPVQSLARSLQEAAGYAISFEEAMRQASSASAYGFDAEQLNKFGLVARRAAAVLGVDMTDALNRVIKGVSKQEIELLDELGVTIRLNDAYADYVKQLNAANTGITYNINSLTTFQKQQAYANAVIAESTKRFGYLDEVLRATPWEQFAANADAALRTIQQAAAKYLGPVIDAINTVFYTSQASISAEAARAQEQTNKQIDPTNVGAVALSLSASEEGYNKALDMYKESLDKRNKLKSEFDKRMEQADFYTKLAIRQVGEGIPAGLATAGASEANKKFVEETAAMGLQVARLDKEVTDSTENLNAWKSAYQAAGAAAAKANPEFQKQINLQRDTTDPGAVYDFNSTVLKGLTEQQKAYNQTKKTASDLANDIQNVAQNTDTAAKTSATLADAIKNIESLSLGTGKSADEYVKNLNLGYNTLSEMKTASQALSEYVKLTGNETKNQLAVQQKIADVYNQTKDKEKAQEAGRRLELQQLEEQEAALRRVLQTNQGNKAVEREIEKIQLEKIKLTNQGMEAQKKVKDYTDKILGVDREIALLNNRTMTDTQYRLAQLNLELTIEKEKYEWYTKQADKQKEAEQSRRAQAQIEREIWKFHQDQQAEMTSKRQEAFENTLTSMFPLAGEMQKMEMQLDFYTQMKELTKDNANEQMRWNAEIAKTRAQMSALTAQRNAQMQSSVGSSLGAVYTPTTGLSGEDKKFADMGNQLASYDQAISKLSELNSEATAVAQSMGNLANAMIQFSQGSLDTTSTIAVGMQTVASMIQYSTSQQVSAIDQAIAAEQKRDGKSEASKAKLKKLEAEKLKIQQDAAKKQIIIQTAVAVMQAATAVPYPFSIPLMIAAGLAGALALAQASSASGMSSIGDSGADTASYLTLGERQKNIDVSMSANAGELSYVRGDKGIGNANSFVPRAEGGNMYPGVSYQMGEHGTEVVTPMVPMKATPNDELKNSSNSTAGRPIILNISAMDAASFREFASSNSGALRDAVELALNENGASLKTLGNS

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7. 引用文献 (1)

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分辨率 resolution	3.20 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	34102

fit	/app/data/saxs_computation/hq/8hqo/8hqo.fit
pddf	/app/data/pr_computation/hq/8hqo/8hqo.pr.out
profile	/app/data/saxs_computation/hq/8hqo/8hqo.dat

Neck of DT57C bacteriophage in the full state

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 (4)

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

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)