SAXSdb — 1jsm

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1jsm
沉积日期 deposition_date	2001-08-17
结构标题 title	STRUCTURE OF H5 AVIAN HAEMAGGLUTININ
关键词 keywords	influenza, receptor complex, fusion protein, Viral protein; VIRAL PROTEIN
实验方法 method	X-RAY DIFFRACTION

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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	36.39 Å
回转半径 Rg (电子) rg_electron	36.76 Å
零角强度 I(0) i0	50435300.00
分子量 molecular_weight	54506.0 kDa
排除体积 excluded_volume	67348 Å³
包络体积 envelope_volume	90979 Å³
水化壳体积 shell_volume	24332 Å³
包络直径 envelope_diameter	132.5 Å
壳层 Rg shell_rg	35.73 Å
包络 Rg envelope_rg	36.89 Å
形状 Rg shape_rg	36.80 Å
总 Rg total_rg	36.57 Å
总原子数 total_atoms	3834
残基数 n_residues	481
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	134.5 Å
Rg (实空间) rg_real	37.18 Å
Rg 误差 (实空间) rg_real_error	2.07 Å
I(0) (实空间) i0_real	5.0440e+07
I(0) 误差 (实空间) i0_real_error	1.0030e+06
Rg (倒空间) rg_reciprocal	36.70 Å
I(0) (倒空间) i0_reciprocal	50410000.0000
解质量估计 total_estimate	0.6718
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	25.0 Å
偏度 Skewness skewness	0.633
峰度 Kurtosis kurtosis	-0.492
角度范围 angular_range	— – 0.2150 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	3965000.0000
实空间数据点数 n_real_points	44
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.260; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.048; Smooth: 0.900

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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 (5)

Entity 1 polymer

描述 description	HAEMAGGLUTININ (HA1 CHAIN)
分子量 formula_weight	36573.2 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	A
原子数 atom_count	4130

DQICIGYHANNSTEQVDTIMEKNVTVTHAQDILEKTHNGKLCDLNGVKPLILRDCSVAGWLLGNPMCDEFLNVPEWSYIVEKDNPVNGLCYPENFNDYEELKHLLSSTNHFEKIRIIPRSSWSNHDASSGVSSACPYNGRSSFFRNVVWLIKKNNAYPTIKRSYNNTNQEDLLILWGIHHPNDAAEQTKLYQNPTTYVSVGTSTLNQRSVPEIATRPKVNGQSGRMEFFWTILKPNDAINFESNGNFIAPEYAYKIVKKGGSAIMKSGLEYGNCNTKCQTPMGAINSSMPFHNIHPLTIGECPKYVKSGRLVLATGLRNVPQRET

Entity 2 polymer

描述 description	HAEMAGGLUTININ (HA2 CHAIN)
分子量 formula_weight	20200.2 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	B

GLFGAIAGFIEGGWQGMVDGWYGYHHSNEQGSGYAADKESTQKAIDGTTNKVNSIIDKMNTQFEAVGKEFNNLERRIENLNKKMEDGFLDVWTYNAELLVLMENERTLDFHDSNVKNLYDKVRLQLRDNAKELGNGCFEFYHKCDNECMESVKNGTYDYPQYSEEARLNREEISGV

Entity 3 branched

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	424.4 kDa
来源方法 src_method	man
拷贝数 entity_count	2

Entity 4 non-polymer

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	221.2 kDa
来源方法 src_method	man
拷贝数 entity_count	3

Entity 5 water

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	296

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6. 折叠分类 (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d1jsma_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.19 — Viral protein domain
超家族 Superfamily superfamily	b.19.1 — Viral protein domain
家族 Family family	b.19.1.2 — Influenza hemagglutinin headpiece

结构域编号 domain_id	d1jsmb_
类 Class class	h — Coiled coil proteins
折叠类型 Fold fold	h.3 — Stalk segment of viral fusion proteins
超家族 Superfamily superfamily	h.3.1 — Influenza hemagglutinin (stalk)
家族 Family family	h.3.1.1 — Influenza hemagglutinin (stalk)

CATH v4.4 (3 domains)

结构域编号 domain_id	1jsmA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	209 — Hemagglutinin (Ha1 Chain); Chain: A; domain 1
同源超家族 H-superfamily homologous superfamily	20 — Haemagglutinin, alpha/beta domain, HA1 chain

结构域编号 domain_id	1jsmA02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	10 — Ribbon
拓扑 Topology topology	77 — Hemagglutinin; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Hemagglutinin Chain A, Domain 2

结构域编号 domain_id	1jsmB00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	20 — Hemagglutinin Ectodomain; Chain B
同源超家族 H-superfamily homologous superfamily	10 —

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7. 引用文献 (1)

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晶胞边长 a length_a	130.728 Å
晶胞边长 b length_b	130.728 Å
晶胞边长 c length_c	254.714 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	120.00 °
晶胞分子数 Z z_pdb	18

空间群 space_group	H 3 2
空间群编号 int_tables_number	155
晶系 crystal_system	—

分辨率 resolution	1.900 Å
最低分辨率 resolution_low	40.000 Å
R 因子 r_factor	0.2340
R_work r_work	0.2340
R_free r_free	0.2640

fit	/app/data/saxs_computation/js/1jsm/1jsm.fit
pddf	/app/data/pr_computation/js/1jsm/1jsm.pr.out
profile	/app/data/saxs_computation/js/1jsm/1jsm.dat

STRUCTURE OF H5 AVIAN HAEMAGGLUTININ

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

衍射实验 Diffraction

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 branched

Entity 4 non-polymer

Entity 5 water

6. 折叠分类 (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)