1ruy

1930 Swine H1 Hemagglutinin

Method: X-RAY DIFFRACTION D_max: 136.7 Å Quality: GOOD

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

下载 Download SAXS (.dat) P(r) (.pr.out) CIF

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1ruy
沉积日期 deposition_date	2003-12-12
结构标题 title	1930 Swine H1 Hemagglutinin
关键词 keywords	Hemagglutinin, INFLUENZA A VIRUS, 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	41.38 Å
回转半径 Rg (电子) rg_electron	40.84 Å
零角强度 I(0) i0	420255000.00
分子量 molecular_weight	163670.0 kDa
排除体积 excluded_volume	203020 Å³
包络体积 envelope_volume	264130 Å³
水化壳体积 shell_volume	55230 Å³
包络直径 envelope_diameter	136.2 Å
壳层 Rg shell_rg	44.64 Å
包络 Rg envelope_rg	40.48 Å
形状 Rg shape_rg	40.85 Å
总 Rg total_rg	41.01 Å
总原子数 total_atoms	11532
残基数 n_residues	1446
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	136.7 Å
Rg (实空间) rg_real	41.54 Å
Rg 误差 (实空间) rg_real_error	1.31 Å
I(0) (实空间) i0_real	4.2030e+08
I(0) 误差 (实空间) i0_real_error	7.3220e+06
Rg (倒空间) rg_reciprocal	41.38 Å
I(0) (倒空间) i0_reciprocal	420200000.0000
解质量估计 total_estimate	0.8517
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	43.2 Å
偏度 Skewness skewness	0.453
峰度 Kurtosis kurtosis	-0.439
角度范围 angular_range	— – 0.1900 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	39860000.0000
实空间数据点数 n_real_points	39
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.823; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.610

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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	hemagglutinin
分子量 formula_weight	36120.5 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	H,J,L
原子数 atom_count	11966

ADADDTLCIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDSHNGKLCRLGGIAPLQLGKCNIAGWLLGNPECDLLLTVSSWSYIVETPNSDNGTCYPGDFIDYEELREQLSSVSSFERFEIFPKTSSWPNHNTNKGVTAACPYAGASSFYRNLLWLVKKGNSYPKLSKSYVNNKGKEVLVLWGVHHPPTSTDQQNLYQNADAYVSVGSSKYNRRFTPEIAARPKVRGQAGRMNYYWTLLEPGDTITFEATGNLVAPRYAFALNRGSGSGIIISNAPVHDCNTKCQTPHGAINSSLPFQNIHPVTIGECPKYVKSTKLRMATGLRNIPAR

Entity 2 polymer

描述 description	hemagglutinin
分子量 formula_weight	18223.1 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	I,K,M

GLFGAIAGFIEGGWTGLIDGWYGYHHQNEQGSGYAADQKSTQNAIDGITNKVNSVIEKMNTQFTAVGKEFNKLEKRIENLNNKVDDGFLDIWTYNAELLVLLENERTLDFHDSNVKNLYEKVRSQLKNNAKEIGNGCFEFYHKCDNECMESVRNGTYDYP

Entity 3 non-polymer

描述 description	2-acetamido-2-deoxy-alpha-D-glucopyranose
分子量 formula_weight	221.2 kDa
来源方法 src_method	man
拷贝数 entity_count	5

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	4

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	434

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6. 折叠分类 (SCOP + CATH) 15 domains

SCOP 2.08 (6 domains)

结构域编号 domain_id	d1ruyh_
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	d1ruyi_
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)

结构域编号 domain_id	d1ruyj_
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	d1ruyk_
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)

结构域编号 domain_id	d1ruyl_
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	d1ruym_
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 (9 domains)

结构域编号 domain_id	1ruyH01
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	1ruyH02
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	1ruyI00
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 —

结构域编号 domain_id	1ruyJ01
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	1ruyJ02
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	1ruyK00
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 —

结构域编号 domain_id	1ruyL01
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	1ruyL02
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	1ruyM00
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	203.106 Å
晶胞边长 b length_b	83.279 Å
晶胞边长 c length_c	178.234 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	106.67 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	12

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	—

分辨率 resolution	2.700 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.2480
R_work r_work	0.2480
R_free r_free	0.2650

fit	/app/data/saxs_computation/ru/1ruy/1ruy.fit
pddf	/app/data/pr_computation/ru/1ruy/1ruy.pr.out
profile	/app/data/saxs_computation/ru/1ruy/1ruy.dat

1930 Swine H1 Hemagglutinin

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 non-polymer

Entity 4 non-polymer

Entity 5 water

6. 折叠分类 (SCOP + CATH) 15 domains

SCOP 2.08 (6 domains)

CATH v4.4 (9 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)