1f8d

Native Influenza Neuraminidase in Complex with 9-amino-2-deoxy-2,3-dehydro-N-neuraminic Acid

Method: X-RAY DIFFRACTION D_max: 77.7 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	1f8d
沉积日期 deposition_date	2000-06-30
结构标题 title	Native Influenza Neuraminidase in Complex with 9-amino-2-deoxy-2,3-dehydro-N-neuraminic Acid
关键词 keywords	neuraminidase, hydrolase, influenza protein, glycosylated protein, 9-amino-DANA, HYDROLASE-HYDROLASE INHIBITOR COMPLEX; HYDROLASE/HYDROLASE INHIBITOR
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	21.21 Å
回转半径 Rg (电子) rg_electron	20.39 Å
零角强度 I(0) i0	38162500.00
分子量 molecular_weight	45881.0 kDa
排除体积 excluded_volume	56433 Å³
包络体积 envelope_volume	64520 Å³
水化壳体积 shell_volume	25322 Å³
包络直径 envelope_diameter	78.1 Å
壳层 Rg shell_rg	28.15 Å
包络 Rg envelope_rg	21.43 Å
形状 Rg shape_rg	20.35 Å
总 Rg total_rg	21.36 Å
总原子数 total_atoms	3214
残基数 n_residues	388
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	77.7 Å
Rg (实空间) rg_real	21.12 Å
Rg 误差 (实空间) rg_real_error	0.57 Å
I(0) (实空间) i0_real	3.8160e+07
I(0) 误差 (实空间) i0_real_error	5.2430e+05
Rg (倒空间) rg_reciprocal	21.13 Å
I(0) (倒空间) i0_reciprocal	38160000.0000
解质量估计 total_estimate	0.8235
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	27.4 Å
偏度 Skewness skewness	0.317
峰度 Kurtosis kurtosis	0.013
角度范围 angular_range	— – 0.3750 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	15100000.0000
实空间数据点数 n_real_points	69
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.581; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.972; Smooth: 0.986

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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 (7)

Entity 1 polymer

描述 description	NEURAMINIDASE
分子量 formula_weight	43723.8 kDa
EC 编号 ec_number	3.2.1.18
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	3579

RDFNNLTKGLCTINSWHIYGKDNAVRIGEDSDVLVTREPYVSCDPDECRFYALSQGTTIRGKHSNGTIHDRSQYRALISWPLSSPPTVYNSRVECIGWSSTSCHDGKTRMSICISGPNNNASAVIWYNRRPVTEINTWARNILRTQESECVCHNGVCPVVFTDGSATGPAETRIYYFKEGKILKWEPLAGTAKHIEECSCYGERAEITCTCRDNWQGSNRPVIRIDPVAMTHTSQYICSPVLTDNPRPNDPTVGKCNDPYPGNNNNGVKGFSYLDGVNTWLGRTISIASRSGYEMLKVPNALTDDKSKPTQGQTIVLNTDWSGYSGSFMDYWAEGECYRACFYVELIRGRPKEDKVWWTSNSIVSMCSSTEFLGQWDWPDGAKIEYFL

来源 Source

来源生物 organism	Influenza A virus (A/tern/Australia/G70C/1975(H11N9))
NCBI 分类编号 ncbi_taxonomy_id	384509
宿主生物 host_organism	Influenza A virus

Entity 2 branched

描述 description	;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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	1235.1 kDa
来源方法 src_method	man
拷贝数 entity_count	1

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	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	1

Entity 5 non-polymer

描述 description	CALCIUM ION
分子量 formula_weight	40.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 6 non-polymer

描述 description	9-AMINO-2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID
分子量 formula_weight	290.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 7 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	363

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6. 折叠分类 (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

结构域编号 domain_id	d1f8da_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.68 — 6-bladed beta-propeller
超家族 Superfamily superfamily	b.68.1 — Sialidases
家族 Family family	b.68.1.1 — Sialidases (neuraminidases)

CATH v4.4 (1 domains)

结构域编号 domain_id	1f8dA00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	120 — 6 Propeller
拓扑 Topology topology	10 — Neuraminidase
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	180.740 Å
晶胞边长 b length_b	180.740 Å
晶胞边长 c length_c	180.740 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	48

空间群 space_group	I 4 3 2
空间群编号 int_tables_number	211
晶系 crystal_system	—

分辨率 resolution	1.400 Å
最低分辨率 resolution_low	10.000 Å
R 因子 r_factor	—
R_work r_work	0.2010
R_free r_free	0.2310

fit	/app/data/saxs_computation/f8/1f8d/1f8d.fit
pddf	/app/data/pr_computation/f8/1f8d/1f8d.pr.out
profile	/app/data/saxs_computation/f8/1f8d/1f8d.dat