SAXSdb — 23sh

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	23sh
沉积日期 deposition_date	2026-02-15
结构标题 title	The composite Cryo-EM structure of the tail region of bacteriophage RAN69
关键词 keywords	bacteriophage, RAN69, tail, VIRUS; VIRUS
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	87.42 Å
回转半径 Rg (电子) rg_electron	88.32 Å
零角强度 I(0) i0	3813420000.00
分子量 molecular_weight	517890.0 kDa
排除体积 excluded_volume	645200 Å³
包络体积 envelope_volume	1108800 Å³
水化壳体积 shell_volume	113120 Å³
包络直径 envelope_diameter	309.5 Å
壳层 Rg shell_rg	71.85 Å
包络 Rg envelope_rg	86.93 Å
形状 Rg shape_rg	88.33 Å
总 Rg total_rg	88.10 Å
总原子数 total_atoms	36509
残基数 n_residues	4799
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	234.1 Å
Rg (实空间) rg_real	83.55 Å
Rg 误差 (实空间) rg_real_error	0.98 Å
I(0) (实空间) i0_real	3.6710e+09
I(0) 误差 (实空间) i0_real_error	7.0610e+07
Rg (倒空间) rg_reciprocal	84.43 Å
I(0) (倒空间) i0_reciprocal	3779000000.0000
解质量估计 total_estimate	0.8962
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	117.1 Å
偏度 Skewness skewness	0.189
峰度 Kurtosis kurtosis	-0.766
角度范围 angular_range	— – 0.0900 Å⁻¹
当前正则化参数 α current_alpha	0.8267
最高正则化参数 α highest_alpha	63270000.0000
实空间数据点数 n_real_points	19
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.941; Stabil: 0.976; Sysdev: 1.000; Positv: 1.000; Valcen: 0.899; Smooth: 0.000

▶

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	tail spike gp1
分子量 formula_weight	60926.1 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	B,J,O
原子数 atom_count	36509

MALVDVVRAGGYSIEYPQFSSMAKLKAFPHSEDGQLVRLLSWHEGVGLGGGLFKVSTSSTATGNDGTVVVASNGVRLLRVVNGPIWADMFGALPNSDIDSKPAVAAAYAYAASVNTDLYIGVAAYKFKGSTPINVDPSRAGIIGYQGKVRIDCSEFTGSVVFSINSSYSYTPAAYYNNLSPALQGLYVFGAKTSGVDGLLVGRETVGSDESYNGQTEVRECTFDKFDRNIRMGHNSWRFVFYKVNSLNALNPNGILYVPAGLDDSGEILSFYHCQFFDGAGSNIRLSCSSYTMVFNTCSFLNITFFVDSASSATVTCNGCNFENPGSASTRRYVDISAGHTNVFNIIGGSIVTNSNPGQTQALLYVSTDNLLNLVGVTVPYGGHYQQEQELGYHAFIGGAGTVTTSGVMLQLRNGAGTCPLHPSLSTFSNWDFGYGNLNAWTVDKGTGTSSVVEYLANAGPKGTEGAMRVAPVSVGTNVSQVQAVTNPGMFSMSCMVNIATTPGNAGQVSIGFLDAAGNRLPGGVSANLGTTTGWKVIGKNTLRGKVPIGAKQVRVNIQTVAGADVKYAYLLCNVVK

Entity 2 polymer

描述 description	nozzle gp13
分子量 formula_weight	86632.8 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	T

MAQSLEGTIQSLLQGVSQQVPRERQPGQLGAQLNMLSDPVSGIRRRPPGEIVWESTIDNPGLDSLFTEYVERGTDGRHMLINTSNGNWWLLAKNGKTVVNSGNDPYFIATAGQTSLQTASIAGLTYILNTEMAPVTAVDNTGRIDPSTTGFFYVKAAAFQKRWEVTVTWSGGSVTGYYNVPDASSGTESAEWASASFVINALINGDPNGYGIGAAITAAGGTVVGFGAYMYIAGLPNLVVSTSSGDTYAVASGQSRVPQEQDLPAQLPAEADGAMCRVGTASSETAWYQFNYSERTWYEVGAYGSITKITNMPRELAADDNIIARDWEGRLAGNDDNNSNPGFIENGYITGIAAFQGRLVLLSGSSVDMSASGLYQRFYRSTVTSLLDTDRISISSASAQDSVYRTAVQFNRDLVLFANSMQAVVPGSAVLTPTNASISITSTYDCDSRVTPVMAGQTVIYPNKRNDSYAGILELIPSPYTAAQYTTQDATVHLPRYIPGRVLQMQNSSVTNMAFSRMSGERNSLLVYEFMWGGSDGAKMQAAWHKWSFPYPILSVQALEDEVFLYMQGPSPSNKLLIVSMDPREGYQLGSEYREAYSDLQKQVQVQDGVFTVPAVLRPVGWADNYKEELILTYLPSNPMGPTEVGIKEIAGENTLRVVRGVPDGTYVIGRRYRSTFTLTTPILRDQNDKLVGSGHVRLLRLDVAVRNSGHFDVQVLDTPRDVNWGGELTGILMNSKELTLGQALRMDLATITVPCRTNADTTEVTLFTEGSMELNVLDISYILRYNQRRRRI

Entity 3 polymer

描述 description	tail fiber gp9
分子量 formula_weight	32818.3 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	r,i,n

MAYSWQEQIKPAGTQDIQCDIEYLDKSYIHVYLDGVETTGYTWTSSTNIRLNTALTVNTTVLLIRKTEREYLYIEFASGSPFIEVNVDSQNTQFLHLAQELVEGRAIPGFYGTISMNGYRITDLANPTNSQDAATKAYVDAADALLGQRIDAEAATRKAADDALSMRTSALENTFISGVETVSYPWSTVLAEATDEVTPGLAFTKAVVEINGVGQIRGYSFEIIDNTILFAETLPAGTVVAARLGADVTAGDGFATQASVDYLADSLGDLAYLDTAEAVPDATGAGDVVAQLNALLASLRTSGVLAS

Entity 4 polymer

描述 description	adaptor gp14
分子量 formula_weight	21286.9 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	Y,d

MRELDAINLTLEALGESRVMDINTSNPSAGLARSALARNRRGLLSTGFWFNVVEREVAPTADGFIKVPWNQLAVYDAGSDSKYGVRDGNLYDLMEQDQYFDSSVKLKIVLDLDFEDLPEHAAMWVANYTTAQVYLNDLGGDSNYANYAQEAERYKSMVLREHLRNQKFSTSKTRFARRIRRARFMV

Entity 5 polymer

描述 description	portal gp19
分子量 formula_weight	58217.7 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	w,0

MEQKATLAELFKKDQDAGVLDASEKFAQWTLSTIFTRDDSLDGRRRPLERDYQSTGAQLVNTAATKIVGALFPQGTSFFRFSKSSDLDEFISSLGSAATAESKLAEVENTASQKVFEKDGYAAKLQAVKLLLVTGNALEYIDERTGKSIVYSVRNFTVRRDGSGNVLRLIIRERASVQDLPEDFRGTFYRDKDPYGDVDIYTAACRKVKRTEDGAEVVSYEVYQEADGHRIGDSSTYPELELPYNVLVWNLVSGEHYGRGLVEDYAGDFARLSVLSEALTNYEVESARLIPLIDASSGLDVDEFSTSETGEAVQVGGGGSNGNSKSPVTAYEGGSAQKIQWIASNIQMLEQKLSRAFMYTGNSRQGERVTAYEIRQNAKEAEAAMGGGFSILSDTWLRKLAYLYTALVYPRFKLYLSEGVVNINVTVGTSALAKAAAADKLLEAAQSMQLAIPVLEQITPRFNKDACVDWYFDAYGIVSEPFMYTEEQLQQKQKVQDASADVSAGAAQDQLQGLTAADPTVAGKQLGLLPS

▶

7. 引用文献 (1)

▶

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	3.200 Å
最低分辨率 resolution_low	— Å
R 因子 r_factor	—
R_work r_work	—
R_free r_free	—

分辨率 resolution	3.20 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	53029

fit	/app/data/saxs_computation/3s/23sh/23sh.fit
pddf	/app/data/pr_computation/3s/23sh/23sh.pr.out
profile	/app/data/saxs_computation/3s/23sh/23sh.dat

The composite Cryo-EM structure of the tail region of bacteriophage RAN69

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

精修参数 Refinement

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)