SAXSdb — 8gtc

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8gtc
沉积日期 deposition_date	2022-09-08
结构标题 title	Cryo-EM model of the marine siphophage vB_DshS-R4C baseplate-tail complex
关键词 keywords	;Marine bacteriophage, Cryo-EM, Siphophage, Baseplate, Megatron protein, Tail fibre protein, Distal tail protein, Hub protein, VIRAL PROTEIN ;; VIRAL PROTEIN
实验方法 method	ELECTRON MICROSCOPY

▼

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	80.35 Å
回转半径 Rg (电子) rg_electron	80.56 Å
零角强度 I(0) i0	9441340000.00
分子量 molecular_weight	506880.0 kDa
排除体积 excluded_volume	498840 Å³
包络体积 envelope_volume	1601700 Å³
水化壳体积 shell_volume	175500 Å³
包络直径 envelope_diameter	269.0 Å
壳层 Rg shell_rg	71.24 Å
包络 Rg envelope_rg	76.66 Å
形状 Rg shape_rg	80.56 Å
总 Rg total_rg	80.45 Å
总原子数 total_atoms	36147
残基数 n_residues	9033
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

▼

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	275.1 Å
Rg (实空间) rg_real	83.28 Å
Rg 误差 (实空间) rg_real_error	1.55 Å
I(0) (实空间) i0_real	9.4410e+09
I(0) 误差 (实空间) i0_real_error	2.3140e+08
Rg (倒空间) rg_reciprocal	80.02 Å
I(0) (倒空间) i0_reciprocal	9432000000.0000
解质量估计 total_estimate	0.6401
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	101.4 Å
偏度 Skewness skewness	0.484
峰度 Kurtosis kurtosis	-0.114
角度范围 angular_range	— – 0.0950 Å⁻¹
当前正则化参数 α current_alpha	1.0850
最高正则化参数 α highest_alpha	557000000.0000
实空间数据点数 n_real_points	20
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.856; Stabil: 0.903; Sysdev: 0.008; Positv: 1.000; Valcen: 0.987; Smooth: 0.144

▶

4. 晶体学与实验 4. Crystallography & Experiment

▶

5. 实体与聚合体信息 (5)

Entity 1 polymer

描述 description	Major tail protein
分子量 formula_weight	13574.8 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	A,B,C,D,E,F
原子数 atom_count	36147

MLKGKDGVVKNASTGDSIGHLQSWALDTQRDEVSGWGMGDDAERAFTTVGRASGNFEVYLDPADPSDDLEPGDLVDLELYPGGESTGSGYRSVAGALILSTAESASKDGIPMLTVNWRTSGALPQKATVS

Entity 2 polymer

描述 description	Distal tail protein
分子量 formula_weight	23378.3 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	G,H,I,J,K,L

MQFIDVEFPRDIAAGCQAVLTRRDEVVTLASGREEVNSRWADTRRSWDAGLGVRDEADLAQVVALFEEVRGRLYAFRFRDWLDWRTAATRAPITATDQPLGLGDGSRTAFQVVKVYGAVNPYTRPLSLPHPGTVRVALDGVTQPSGWTLTAPGGVITFDTPPALGVTVTAGCSFDVPVRFSDPELAVQWAYFREGQAGLAQAPSIPLIEVRLDP

Entity 3 polymer

描述 description	Megatron protein
分子量 formula_weight	154569.1 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	M,N,O

MATVLLAAAGGAIGTSLGGALFGISAAVIGQAVGGLIGQTIDARLSGGGTIKQTGPRLDSLEVMVSQEGTPLADISGRVAVAGTVIWATKLEEIARTTSTRVGSGKSSQKVKSTNFDYAASFAVSLGEGPLNGIGRIFLDGQVRDLSEMISENRVRFYPGTEDQEPDPLIEAIEGAAPAFRGTAYLVFERLFLSDFGNRVPQVRVEVFGQSGEMEKGVTGVCVIPGSTEFGYMPAPVRQQSLDGADVVWEGPENCNRYSRISDWSLSMDHLKNTLPAVQTVSLVVAWFGTDLRAGLCRFEPRIELRAKRTSIEWIAAGLNRGSATEVSRDENDRPAFGSSPADVSVVRAIMDLKARGFRVVLYPFVMMDVTADQALPSPAGTGAQGAYPWRGRIMPDVTGGRVSDQIAALMGTAQPDDFTAAVTRNKSGEISQVNLTCPGAPGDAGLRRFILHLAKLADIAGGVDAFLVGTEFRGLSQAWEPQTYADAYEFLNSSEGWFAQNAARTHEPGSLLVSATARDPRLISPPLSIDGAAARWIEIEFDRTSAPVWEGNVYYMTEDHGFAGAFRKVISDAEAPADGTRARMLLDMHDLTLGGDDWRTSTITRLRFDFSSESDAVFRIHAIRLGGGRRYPFVDALRDLAQDVDTILPTAKISYAADWSEYHSHQDAGDLTFHLDPLWADPAIDFVGIDNYLPLSDWRQGADHLDYDATSGRTTPYDLDYLKSNIEGGEYWDWFYASQEDRDTQTRTPISDGSYGEPWVFRQKAIRDWHANAHHNRTAGVRATTSTGWVPGSKPVWFTEYGCPAVDLGANRPNVFAAASSSESALPWYSSGLRDDFMQRQYLRAMAEWWTANGAPAVDLANCQAWAWDARPFPEFPLRPATWSDGPDWRLGHWLNGRAGAAPAAEAITRRAITRHGLISADIDTSRAYGQADGYAAPAPLGLGDYAQPFEVALGLQTTETGGALVIEAKPAAPLAADVIEADLVDTPAIYTLTRGALEDTPAAAIVRFRDGLSDYEITAARARIGAGKEGGSATADLALVLDGDRGNAAAEMVLRAALTSRESLSVTLPRSATTLRPGSLVEVTLGTEARRLFLVDRVVDGQAREVTLRGFDRAAYAPSGGVFKAARAGRLQGSTSSLTRFLDLPLLPGVDAPEWEGFIAAHAEPWPGAMLHSRGSTPEGSFTLAAEADARATIGRTTAALPPAPAHVWTPGPLVVTLFSGALVGRPDLDVLDGANALAIQHPDGWEVVQFREATLTADRTWRLEGLLRGQRGTDGIVGPAPLPAGAAVVAIDTALVAAGLSADDPGRALWWRSGPDAASLAAAPLRPHTFTAAGLRAFPPAHLRAVVTGGGDTSLSWVPRSRLVGTTWPDNGAPIPSGEGLERYQVTIGPTAAPVRVILADTPAATYTAAERAADGIAAPFRVAVSQISETTGPGPWIETIVTE

Entity 4 polymer

描述 description	Hub protein
分子量 formula_weight	31055.4 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	P,Q,R

MTDYTDHLATGCTTLARCYILTRRDGVVMGFTDHDRDIDLDGTRCAAGAALDASTAARSLGITPDDMDAGGALSADAITEADLRAGRYDGAQVEVWEVNWTDPAVRGRLGVYTIGQVERGPLAFRAELRTRPALWNRPEGRIHTALCDVDRLGDHRCKLALGPWQSAATVIEADGADLIVSGLDETASNIFDRGVLDWTGGANAGTGSDIRVARPVAGGVRVSLWSAPPFPITAGDTANATVGCDRTADTCRNRFDNLANFRGFPLMPGESFISEYARPGDPDQSGGSRYD

Entity 5 polymer

描述 description	Ribonuclease III
分子量 formula_weight	22783.8 kDa
来源方法 src_method	nat
拷贝数 entity_count	9

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	S,T,U,V,W,X,Y,Z,a

MPTPFLALPLIAEGQAGQHVTHNEALDMIDALAPRVVLSDSLATPPPAPPDRSAWIVPPGGSGFGGAGPGQIALRLGGVWHAITPAQGARWRVLDRGAAVIWSGTSWRPADVSGALGSTLGLATIEATVTATGPSVTAPALIPPRAIVLGVTSWTVQAVTGATSYRVGVPGEPDKFGASLGAAPGSSNIGVVGPFATYAPTDVVVTAEGADFTGGTIGLAASVILPGAPV

▶

7. 引用文献 (1)

▶

分辨率 resolution	4.50 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	11598

fit	/app/data/saxs_computation/gt/8gtc/8gtc.fit
pddf	/app/data/pr_computation/gt/8gtc/8gtc.pr.out
profile	/app/data/saxs_computation/gt/8gtc/8gtc.dat

Cryo-EM model of the marine siphophage vB_DshS-R4C baseplate-tail complex

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 (5)

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

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)