SAXSdb — 1l7f

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1l7f
沉积日期 deposition_date	2002-03-15
结构标题 title	Crystal structure of influenza virus neuraminidase in complex with BCX-1812
关键词 keywords	N9 neuraminidase, hydrolase, influenza, glycosylated protein, BCX-1812; HYDROLASE
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	21.26 Å
回转半径 Rg (电子) rg_electron	20.43 Å
零角强度 I(0) i0	38599200.00
分子量 molecular_weight	46196.0 kDa
排除体积 excluded_volume	56879 Å³
包络体积 envelope_volume	64824 Å³
水化壳体积 shell_volume	25421 Å³
包络直径 envelope_diameter	78.7 Å
壳层 Rg shell_rg	28.13 Å
包络 Rg envelope_rg	21.39 Å
形状 Rg shape_rg	20.39 Å
总 Rg total_rg	21.40 Å
总原子数 total_atoms	3235
残基数 n_residues	385
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	77.6 Å
Rg (实空间) rg_real	21.17 Å
Rg 误差 (实空间) rg_real_error	0.53 Å
I(0) (实空间) i0_real	3.8600e+07
I(0) 误差 (实空间) i0_real_error	4.7890e+05
Rg (倒空间) rg_reciprocal	21.19 Å
I(0) (倒空间) i0_reciprocal	38600000.0000
解质量估计 total_estimate	0.6462
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	27.4 Å
偏度 Skewness skewness	0.310
峰度 Kurtosis kurtosis	0.003
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	15140000.0000
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: 0.589; Stabil: 1.000; Sysdev: 0.225; Positv: 1.000; Valcen: 0.975; Smooth: 0.982

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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 (8)

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	nat
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	3895

RDFNNLTKGLCTINSWHIYGKDNAVRIGEDSDVLVTREPYVSCDPDECRFYALSQGTTIRGKHSNGTIHDRSQYRALISWPLSSPPTVYNSRVECIGWSSTSCHDGKTRMSICISGPNNNASAVIWYNRRPVTEINTWARNILRTQESECVCHNGVCPVVFTDGSATGPAETRIYYFKEGKILKWEPLAGTAKHIEECSCYGERAEITCTCRDNWQGSNRPVIRIDPVAMTHTSQYICSPVLTDNPRPNDPTVGKCNDPYPGNNNNGVKGFSYLDGVNTWLGRTISIASRSGYEMLKVPNALTDDKSKPTQGQTIVLNTDWSGYSGSFMDYWAEGECYRACFYVELIRGRPKEDKVWWTSNSIVSMCSSTEFLGQWDWPDGAKIEYFL

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)]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	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	3-(1-ACETYLAMINO-2-ETHYL-BUTYL)-4-GUANIDINO-2-HYDROXY-CYCLOPENTANECARBOXYLIC ACID
分子量 formula_weight	328.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 7 non-polymer

描述 description	GLYCEROL
分子量 formula_weight	92.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 8 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	642

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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	d1l7fa_
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	1l7fA00
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 (3)

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晶胞边长 a length_a	181.122 Å
晶胞边长 b length_b	181.122 Å
晶胞边长 c length_c	181.122 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	1.800 Å
最低分辨率 resolution_low	6.000 Å
R 因子 r_factor	—
R_work r_work	0.1530
R_free r_free	0.1870

fit	/app/data/saxs_computation/l7/1l7f/1l7f.fit
pddf	/app/data/pr_computation/l7/1l7f/1l7f.pr.out
profile	/app/data/saxs_computation/l7/1l7f/1l7f.dat

Crystal structure of influenza virus neuraminidase in complex with BCX-1812

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution