SAXSdb — 9d80

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	9d80
沉积日期 deposition_date	2024-08-18
最后修订 last_revision	2025-01-15
结构标题 title	Shigella flexneri bacteriophage Moo19 Tail
关键词 keywords	Moo19, 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	93.44 Å
回转半径 Rg (电子) rg_electron	97.22 Å
零角强度 I(0) i0	315539000.00
分子量 molecular_weight	148370.0 kDa
排除体积 excluded_volume	185490 Å³
包络体积 envelope_volume	462330 Å³
水化壳体积 shell_volume	47692 Å³
包络直径 envelope_diameter	423.2 Å
壳层 Rg shell_rg	60.87 Å
包络 Rg envelope_rg	103.10 Å
形状 Rg shape_rg	97.24 Å
总 Rg total_rg	96.36 Å
总原子数 total_atoms	10448
残基数 n_residues	1331
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	238.6 Å
Rg (实空间) rg_real	82.99 Å
Rg 误差 (实空间) rg_real_error	1.63 Å
I(0) (实空间) i0_real	2.9850e+08
I(0) 误差 (实空间) i0_real_error	6.0990e+06
Rg (倒空间) rg_reciprocal	82.33 Å
I(0) (倒空间) i0_reciprocal	305300000.0000
解质量估计 total_estimate	0.7979
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	42.1 Å
偏度 Skewness skewness	0.308
峰度 Kurtosis kurtosis	-0.847
角度范围 angular_range	— – 0.0850 Å⁻¹
当前正则化参数 α current_alpha	0.0990
最高正则化参数 α highest_alpha	15020000.0000
实空间数据点数 n_real_points	18
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.023; Oscil: 0.519; Stabil: 0.946; Sysdev: 1.000; Positv: 1.000; Valcen: 0.654; Smooth: 0.365

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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	85342.8 kDa
来源方法 src_method	man
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	10448

MEHQDSMTPLPDPGQSDKLTNWKKEPSIQTLKADLEAGKPAHDAIMKEIQKWNDLMKAEGSAKPPKVKGRSQVQPKLVRRQAEWRYAPLSEPFLSSPKLFKLTPVTWEDEQAARQNELVLNYQFRTQLNRVKLVDDYVHSVCDDGTGIARVGWERKVVKVKQDAPVFQMYPVETEEQVQILQQALDLQAQNPRGYEEQVADDVKEAVNYFNETGEATYAIQTGTTEVEVEKAVVNRPTVEMLDPNNVVIDPSCNGDLDRALFAVVSFETCKADLLKTPDRYHNLDKIDWESSSPLTDPDHESKTPGDFQFRDAMRKRVIAYEYWGFWDTNGDGELKPIVATWIGTTLIRMEENPYPDGKLPFVLVPYMPRKRELYGEADAELLGDNQKILGATMRGMIDLLGRSANGQRAYPKGMLDTLNRRRFEDGLDYEYNPQTGNPSQAIIEHKFPELPQSAIVMSQMQNQEAEALTGVKAFAGGVTGSAYGDVAAGIRGALDAASKREMAILRRLAKGMADIGTKICAMNAVFLSETEVVRITNEEYVTINREDLKGNFDIEVDINTAEVDNQKSQDLGFMVQTIGNTVDQQVTLKLVARIAELKRMPELAHELRTWKPEPDPMEEQLKQLAIQKAQLENQKLQSEIALNEAKVRAEDAKKDMTNLDYLEQESGTKHAREMEKQKAQSQGNQNLQVTKALTQPVKEGETSPNISAAIGYNAITDGNNQVNNELERDALAPQDPSLSIGSQYFDPSRDPALSPGMNL

来源 Source

来源生物 organism	Shigella virus Moo19
NCBI 分类编号 ncbi_taxonomy_id	2886042
宿主生物 host_organism	Shigella flexneri 2a str. 2457T

Entity 2 polymer

描述 description	Gp83
分子量 formula_weight	26990.5 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B

MRKLSDVYKVLALTSLKSAGFITDDKVNIEAWGKPEVLAHINEGLTRLHSRFVLRTNNCIVEMKEGRTDYPLLARYSYERFDPAKAPYPYIMDTPQEPFQEDVIKILNVYDSKGIRRKLNDDHDKNGLFTPRPDVLQCMWPRHFEALNVLYQAKHPELTGDENQEIDLPETLYSALENWVGYRYHTGLNTEGSTAKAAEYLQLYESICGEVVDFDLANGSMSNTNVLFEKRGWV

来源 Source

来源生物 organism	Shigella virus Moo19
NCBI 分类编号 ncbi_taxonomy_id	2886042
宿主生物 host_organism	Shigella flexneri 2a str. 2457T

Entity 3 polymer

描述 description	Tail protein
分子量 formula_weight	30295.9 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	C

MSCGAEVEANRLLLALTEGEDFALPDIDMSGPEWDIPGGDGSPIFAEVTRLTNEDLTTRVVGGSGTFDALMASAAAHLKQEFKEGRITGGEYTKAYIAIVETCMGNATQYLLGRDQAYWAAAMAQIQAVSARVALATSKAQYVLAKFQALNAKSEYALTKLKLSTESETYCAALFNVEQTLPQQLKLLIEQTEAQRAQTLDKRSDGATVSGSIGKQKELYTQQITSYQRDAEVKASKLFTDAWITQKTIDEGLTPPNGFTNSSIDDVLTTLKRNNNLNG

来源 Source

来源生物 organism	Shigella virus Moo19
NCBI 分类编号 ncbi_taxonomy_id	2886042
宿主生物 host_organism	Shigella flexneri 2a str. 2457T

Entity 4 polymer

描述 description	Tail fiber protein
分子量 formula_weight	118004.1 kDa
来源方法 src_method	man
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	D,E,F

MGMNSHIPFDADNDWTLDPYHCNRSNDPLVDKVIGNAYAVVRAVYCNLGNLKLLYDFLNTYGMVLGVKSEAELKKLNKLAKYARVYGFADTGDRQVTDYLYVPDDTSGIRPDDQTATGSWIKVSTSGSGSGGTGGGSGSYIPYVYANGSALGGETSFKVPAEALGVPFIIINGSVQYIGYGFSFNPANSTVTLSNPLVQGDEVIALTSAAPASPDNPNVSNWVQVNWLYNNGAAVGGEQVITVPYNFKDVPAVYKNGERYYKNLQTKSYVYDPSTRTVTMTELLAQGDRVIITLGGESASLEITDRTTQEVARANNVKDTDVVLSSSTNVVITDKKVLYDVNAQKYWDLPNLPPNVYIVKVEGNKLIYNPGAVVIDLLEPANPLVIVEPVLSRLGAETGNPMAGTFEKGATVDSAAKSVGSTMEGKLYRWEGALPKTVRAGDTPSSSGGIGSGKWVEITNATLRSQLASTGGAAMVKASDGRTVEQWLVQSDSASFRAKNMAKLAWCDYQVHNRGSLKCCFLGDSMTAGFDRTSSDTIPAQDGDWATRASMNYPYRFASYLPEQSGCSVYITMRAISGYTAKQAYEEALWQSNPNCDIVFIMYAINDSGGVAGATLDLYMEYMEKLIRRYIDWGCAVVVQRPSGGGQGAGNPAWLHWAKRMQMVARVYGCPVFDAHEVMLNRHYAAVQSDGTHYNSMGYAIHGEKLASMLMAGGLLDTYKPVVNETTVWTGMMSDHIGWCDARGNIGTGRSDGAYTRDKVTGVLQAGKATICTFSFYLDAEAAHIYGKLDGLINTIYTNGYWWNNGNKPYYQYAVDIDNSFGASLQRVNKSANNYEGMPGSRKFVGRLIGRGWHTITLFTNLQGEALKDAFVNSITVQPIPIGLSTEQMWGQDEERRYRVVHTRRMPSPSGQGGTLPVAVALTGFQMRAPQSFLGTGPGTNAVPAPYFYNTVPGKLKVYNEKGDYIEWLVYKDGSSGLKWKGKVLTHSFADVASVPTLTAYMGTAKQNVIVAAGSSGANQPLENIYDYNAGLQEQTGNPSTDLSWKGGIYLVFTLAWPSTAPTGYWTIELEGSDWFGNSESAVGCF

来源 Source

来源生物 organism	Shigella virus Moo19
NCBI 分类编号 ncbi_taxonomy_id	2886042
宿主生物 host_organism	Shigella flexneri 2a str. 2457T

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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	3.70 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	95783

fit	/app/data/saxs_computation/d8/9d80/9d80.fit
pddf	/app/data/pr_computation/d8/9d80/9d80.pr.out
profile	/app/data/saxs_computation/d8/9d80/9d80.dat

Shigella flexneri bacteriophage Moo19 Tail

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 (4)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 polymer

聚合体 Polymer

来源 Source

Entity 4 polymer

聚合体 Polymer

来源 Source

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)