SAXSdb — 1ha0

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1ha0
沉积日期 deposition_date	1998-10-08
结构标题 title	HEMAGGLUTININ PRECURSOR HA0
关键词 keywords	GLYCOPROTEIN, MEMBRANE-FUSION PRECURSOR, VIRUS/VIRAL 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	36.89 Å
回转半径 Rg (电子) rg_electron	37.45 Å
零角强度 I(0) i0	55721100.00
分子量 molecular_weight	57403.0 kDa
排除体积 excluded_volume	71016 Å³
包络体积 envelope_volume	93479 Å³
水化壳体积 shell_volume	24885 Å³
包络直径 envelope_diameter	136.9 Å
壳层 Rg shell_rg	35.79 Å
包络 Rg envelope_rg	37.58 Å
形状 Rg shape_rg	37.46 Å
总 Rg total_rg	37.27 Å
总原子数 total_atoms	4033
残基数 n_residues	494
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	134.6 Å
Rg (实空间) rg_real	37.72 Å
Rg 误差 (实空间) rg_real_error	1.80 Å
I(0) (实空间) i0_real	5.5720e+07
I(0) 误差 (实空间) i0_real_error	1.0700e+06
Rg (倒空间) rg_reciprocal	37.21 Å
I(0) (倒空间) i0_reciprocal	55690000.0000
解质量估计 total_estimate	0.6685
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	0.630
峰度 Kurtosis kurtosis	-0.494
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	3793000.0000
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: 0.271; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.052; Smooth: 0.821

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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	PROTEIN (HEMAGGLUTININ PRECURSOR)
分子量 formula_weight	55346.8 kDa
突变 mutation	R329Q
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	4070

STATLCLGHHAVPNGTLVKTITDDQIEVTNATELVQSSSTGKICNNPHRILDGIDCTLIDALLGDPHCDVFQNETWDLFVERSKAFSNCYPYDVPDYASLRSLVASSGTLEFITEGFTWTGVTQNGGSNACKRGPGSGFFSRLNWLTKSGSTYPVLNVTMPNNDNFDKLYIWGIHHPSTNQEQTSLYVQASGRVTVSTRRSQQTIIPNIGSRPWVRGLSSRISIYWTIVKPGDVLVINSNGNLIAPRGYFKMRTGKSSIMRSDAPIDTCISECITPNGSIPNDKPFQNVNKITYGACPKYVKQNTLKLATGMRNVPEKQTQGLFGAIAGFIENGWEGMIDGWYGFRHQNSEGTGQAADLKSTQAAIDQINGKLNRVIEKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTRRQLRENAEEMGNGCFKIYHKCDNACIESIRNGTYDHDVYRNEALNNRFQI

来源 Source

来源生物 organism	Influenza A virus
NCBI 分类编号 ncbi_taxonomy_id	11320
宿主生物 host_organism	Vaccinia virus

Entity 2 branched

描述 description	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	586.5 kDa
来源方法 src_method	man
拷贝数 entity_count	2

Entity 3 branched

描述 description	alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	586.5 kDa
来源方法 src_method	man
拷贝数 entity_count	1

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	2

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	37

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6. 折叠分类 (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d1ha0a1
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	d1ha0a2
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 (2 domains)

结构域编号 domain_id	1ha0A01
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	1ha0A02
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	153.000 Å
晶胞边长 b length_b	153.000 Å
晶胞边长 c length_c	153.000 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	24

空间群 space_group	I 21 3
空间群编号 int_tables_number	199
晶系 crystal_system	—

分辨率 resolution	2.800 Å
最低分辨率 resolution_low	8.000 Å
R 因子 r_factor	0.2240
R_work r_work	0.2240
R_free r_free	0.3020

fit	/app/data/saxs_computation/ha/1ha0/1ha0.fit
pddf	/app/data/pr_computation/ha/1ha0/1ha0.pr.out
profile	/app/data/saxs_computation/ha/1ha0/1ha0.dat

HEMAGGLUTININ PRECURSOR HA0

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