1rvx

1934 H1 Hemagglutinin in complex with LSTA

Method: X-RAY DIFFRACTION D_max: 211.9 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	1rvx
沉积日期 deposition_date	2003-12-15
结构标题 title	1934 H1 Hemagglutinin in complex with LSTA
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	66.30 Å
回转半径 Rg (电子) rg_electron	67.17 Å
零角强度 I(0) i0	1641140000.00
分子量 molecular_weight	333150.0 kDa
排除体积 excluded_volume	413340 Å³
包络体积 envelope_volume	615030 Å³
水化壳体积 shell_volume	81232 Å³
包络直径 envelope_diameter	235.5 Å
壳层 Rg shell_rg	60.37 Å
包络 Rg envelope_rg	65.83 Å
形状 Rg shape_rg	67.18 Å
总 Rg total_rg	67.01 Å
总原子数 total_atoms	23444
残基数 n_residues	2890
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	211.9 Å
Rg (实空间) rg_real	67.27 Å
Rg 误差 (实空间) rg_real_error	1.73 Å
I(0) (实空间) i0_real	1.6400e+09
I(0) 误差 (实空间) i0_real_error	3.2350e+07
Rg (倒空间) rg_reciprocal	65.30 Å
I(0) (倒空间) i0_reciprocal	1635000000.0000
解质量估计 total_estimate	0.7956
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	44.1 Å
偏度 Skewness skewness	0.533
峰度 Kurtosis kurtosis	-0.378
角度范围 angular_range	— – 0.1200 Å⁻¹
当前正则化参数 α current_alpha	0.0019
最高正则化参数 α highest_alpha	137700000.0000
实空间数据点数 n_real_points	25
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.796; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.845; Smooth: 0.107

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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	36733.4 kDa
来源方法 src_method	nat
拷贝数 entity_count	6

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,C,E,G,I,K
原子数 atom_count	25966

ATNADTICIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDSHNGKLCRLKGIAPLQLGKCNIAGWLLGNPECDPLLPVRSWSYIVETPNSENGICYPGDFIDYEELREQLSSVSSFERFEIFPKESSWPNHNTNGVTAACSHEGKSSFYRNLLWLTEKEGSYPKLKNSYVNKKGKEVLVLWGIHHPPNSKEQQNLYQNENAYVSVVTSNYNRRFTPEIAERPKVRDQAGRMNYYWTLLKPGDTIIFEANGNLIAPMYAFALRRGFGSGIITSNASMHECNTKCQTPLGAINSSLPYQNIHPVTIGECPKYVRSAKLRMVTGLRNIPAR

Entity 2 polymer

描述 description	Hemagglutinin
分子量 formula_weight	18242.2 kDa
来源方法 src_method	nat
拷贝数 entity_count	6

聚合体 Polymer

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

GLFGAIAGFIEGGWTGMIDGWYGYHHQNEQGSGYAADQKSTQNAINGITNKVNSVIEKMNIQFTAVGKEFNKLEKRMENLNNKVDDGFLDIWTYNAELLVLLENERTLDFHDSNVKNLYEKVKSQLKNNAKEIGNGCFEFYHKCDNECMESVRNGTYDYP

Entity 3 branched

描述 description	N-acetyl-alpha-neuraminic acid-(2-3)-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	6

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	10

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	2522

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6. 折叠分类 (SCOP + CATH) 30 domains

SCOP 2.08 (12 domains)

结构域编号 domain_id	d1rvxa_
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	d1rvxb_
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	d1rvxc_
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	d1rvxd_
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	d1rvxe_
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	d1rvxf_
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	d1rvxg_
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	d1rvxh_
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	d1rvxi_
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	d1rvxj_
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	d1rvxk_
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	d1rvxl_
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 (18 domains)

结构域编号 domain_id	1rvxA01
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	1rvxA02
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	1rvxB00
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	1rvxC01
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	1rvxC02
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	1rvxD00
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	1rvxE01
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	1rvxE02
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	1rvxF00
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	1rvxG01
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	1rvxG02
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	1rvxH00
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	1rvxI01
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	1rvxI02
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	1rvxJ00
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	1rvxK01
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	1rvxK02
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	1rvxL00
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	227.878 Å
晶胞边长 b length_b	131.344 Å
晶胞边长 c length_c	174.708 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	110.09 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	24

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	2.200 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.2270
R_work r_work	0.2270
R_free r_free	0.2600

fit	/app/data/saxs_computation/rv/1rvx/1rvx.fit
pddf	/app/data/pr_computation/rv/1rvx/1rvx.pr.out
profile	/app/data/saxs_computation/rv/1rvx/1rvx.dat

1934 H1 Hemagglutinin in complex with LSTA

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) 30 domains

SCOP 2.08 (12 domains)

CATH v4.4 (18 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)