9dio

Crystal structure of H5 hemagglutinin Q226L mutant from the influenza virus A/Texas/37/2024 (H5N1) with LSTc

Method: X-RAY DIFFRACTION D_max: 213.8 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	9dio
沉积日期 deposition_date	2024-09-05
结构标题 title	Crystal structure of H5 hemagglutinin Q226L mutant from the influenza virus A/Texas/37/2024 (H5N1) with LSTc
关键词 keywords	H1N1, Antibody, Hemagglutinin, 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	62.91 Å
回转半径 Rg (电子) rg_electron	62.27 Å
零角强度 I(0) i0	3986890000.00
分子量 molecular_weight	520060.0 kDa
排除体积 excluded_volume	644890 Å³
包络体积 envelope_volume	951930 Å³
水化壳体积 shell_volume	125860 Å³
包络直径 envelope_diameter	207.5 Å
壳层 Rg shell_rg	65.20 Å
包络 Rg envelope_rg	60.49 Å
形状 Rg shape_rg	62.30 Å
总 Rg total_rg	62.25 Å
总原子数 total_atoms	36564
残基数 n_residues	4414
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	213.8 Å
Rg (实空间) rg_real	62.73 Å
Rg 误差 (实空间) rg_real_error	2.14 Å
I(0) (实空间) i0_real	3.9870e+09
I(0) 误差 (实空间) i0_real_error	8.2280e+07
Rg (倒空间) rg_reciprocal	63.02 Å
I(0) (倒空间) i0_reciprocal	3989000000.0000
解质量估计 total_estimate	0.8836
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	85.5 Å
偏度 Skewness skewness	0.172
峰度 Kurtosis kurtosis	-0.579
角度范围 angular_range	— – 0.1250 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	536500000.0000
实空间数据点数 n_real_points	26
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.872; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.875

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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 (10)

Entity 1 polymer

描述 description	Hemagglutinin HA1
分子量 formula_weight	36520.4 kDa
来源方法 src_method	man
拷贝数 entity_count	9

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,C,E,G,I,K,M,O,Q
原子数 atom_count	36829

ADPGDQICIGYHANNSTEQVDTIMEKNVTVTHAQDILEKTHNGKLCDLNGVKPLILKDCSVAGWLLGNPMCDEFIRVPEWSYIVERANPANDLCYPGSLNDYEELKHMLSRINHFEKIQIIPKSSWPNHETSLGVSAACPYQGAPSFFRNVVWLIKKNDAYPTIKISYNNTNREDLLILWGIHHSNNAEEQTNLYKNPITYISVGTSTLNQRLAPKIATRSQVNGLRGRMDFFWTILKPDDAIHFESNGNFIAPEYAYKIVKKGDSTIMKSGVEYGHCNTKCQTPVGAINSSMPFHNIHPLTIGECPKYVKSNKLVLATGLRNSP

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	Spodoptera aff. frugiperda 1 BOLD-2017

Entity 2 polymer

描述 description	Hemagglutinin HA2
分子量 formula_weight	20257.3 kDa
来源方法 src_method	man
拷贝数 entity_count	9

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B,D,F,H,J,L,N,P,R

GLFGAIAGFIEGGWQGMVDGWYGYHHSNEQGSGYAADKESTQKAIDGVTNKVNSIIDKMNTQFEAVGREFNNLERRIENLNKKMEDGFLDVWTYNAELLVLMENERTLDFHDSNVKNLYDKVRLQLRDNAKELGNGCFEFYHKCDNECMESVRNGTYDYPQYSEEARLKREEISSG

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	Spodoptera aff. frugiperda 1 BOLD-2017

Entity 3 branched

描述 description	;N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose ;
分子量 formula_weight	836.7 kDa
来源方法 src_method	man
拷贝数 entity_count	3

Entity 4 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	1

Entity 5 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	7

Entity 6 branched

描述 description	N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	674.6 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 7 branched

描述 description	;N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose ;
分子量 formula_weight	998.9 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 8 branched

描述 description	;N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose ;
分子量 formula_weight	836.7 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 9 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	syn
拷贝数 entity_count	16

Entity 10 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	265

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7. 引用文献 (1)

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晶胞边长 a length_a	254.381 Å
晶胞边长 b length_b	214.467 Å
晶胞边长 c length_c	136.040 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	115.08 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	36

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	45.330 Å
R 因子 r_factor	0.2181
R_work r_work	0.2161
R_free r_free	0.2564

fit	/app/data/saxs_computation/di/9dio/9dio.fit
pddf	/app/data/pr_computation/di/9dio/9dio.pr.out
profile	/app/data/saxs_computation/di/9dio/9dio.dat

Crystal structure of H5 hemagglutinin Q226L mutant from the influenza virus A/Texas/37/2024 (H5N1) with LSTc

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 (10)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 branched

Entity 4 branched

Entity 5 branched

Entity 6 branched

Entity 7 branched

Entity 8 branched

Entity 9 non-polymer

Entity 10 water

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)