1usr

Newcastle disease virus hemagglutinin-neuraminidase: Evidence for a second sialic acid binding site and implications for fusion

Method: X-RAY DIFFRACTION D_max: 101.7 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	1usr
沉积日期 deposition_date	2003-11-28
结构标题 title	Newcastle disease virus hemagglutinin-neuraminidase: Evidence for a second sialic acid binding site and implications for fusion
关键词 keywords	HYDROLASE, SIALIDASE, NEURAMINIDASE, HEMAGGLUTININ-NEURAMINIDASE, HEMAGGLUTININ, GLYCOPROTEIN; 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	30.61 Å
回转半径 Rg (电子) rg_electron	29.92 Å
零角强度 I(0) i0	161587000.00
分子量 molecular_weight	99951.0 kDa
排除体积 excluded_volume	124300 Å³
包络体积 envelope_volume	142340 Å³
水化壳体积 shell_volume	39751 Å³
包络直径 envelope_diameter	109.0 Å
壳层 Rg shell_rg	37.22 Å
包络 Rg envelope_rg	30.19 Å
形状 Rg shape_rg	29.90 Å
总 Rg total_rg	30.55 Å
总原子数 total_atoms	7022
残基数 n_residues	895
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	101.7 Å
Rg (实空间) rg_real	30.70 Å
Rg 误差 (实空间) rg_real_error	0.71 Å
I(0) (实空间) i0_real	1.6160e+08
I(0) 误差 (实空间) i0_real_error	2.3540e+06
Rg (倒空间) rg_reciprocal	30.66 Å
I(0) (倒空间) i0_reciprocal	161600000.0000
解质量估计 total_estimate	0.8704
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	33.2 Å
偏度 Skewness skewness	0.454
峰度 Kurtosis kurtosis	-0.303
角度范围 angular_range	— – 0.2600 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	43740000.0000
实空间数据点数 n_real_points	53
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.812; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.971; Smooth: 0.904

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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	HEMAGGLUTININ-NEURAMINIDASE GLYCOPROTEIN
分子量 formula_weight	49856.9 kDa
EC 编号 ec_number	3.2.1.18
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	7943

GAPIHDPDFIGGIGKELIVDNASDVTSFYPSAFQEHLNFIPAPTTGSGCTRIPSFDMSATHYCYTHNVILSGCRDHSHSHQYLALGVLRTTATGRIFFSTLRSISLDDTQNRKSCSVSATPLGCDMLCSKVTETEEEDYNSAVPTLMAHGRLGFDGQYHEKDLDVTTLFEDWVANYPGVGGGSFIDGRVWFSVYGGLKPNSPSDTVQEGKYVIYKRYNDTCPDEQDYQIRMAKSSYKPGRFGGKRIQQAILSIKVSTSLGEDPVLTVPPNTVTLMGAEGRILTVGTSHFLYQRGSSYFSPALLYPMTVSNKTATLHSPYTFNAFTRPGSIPCQASARCPNSCVTGVYTDPYPLIFYRNHTLRGVFGTMLDSEQARLNPASAVFDSTSRSRITRVSSSSTKAAYTTSTCFKVVKTNKTYCLSIAEISNTLFGEFRIVPLLVEILKNDGVREARSG

Entity 2 branched

描述 description	N-acetyl-alpha-neuraminic acid-(2-6)-methyl 6-thio-beta-D-galactopyranoside
分子量 formula_weight	501.5 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 3 non-polymer

描述 description	2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID
分子量 formula_weight	291.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 non-polymer

描述 description	2-acetamido-2-deoxy-alpha-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 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	N-acetyl-alpha-neuraminic acid
分子量 formula_weight	309.3 kDa
来源方法 src_method	man
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	921

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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	d1usra_
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)

结构域编号 domain_id	d1usrb_
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 (2 domains)

结构域编号 domain_id	1usrA00
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 —

结构域编号 domain_id	1usrB00
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	175.480 Å
晶胞边长 b length_b	99.260 Å
晶胞边长 c length_c	64.330 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	8

空间群 space_group	P 21 21 2
空间群编号 int_tables_number	18
晶系 crystal_system	—

分辨率 resolution	2.000 Å
最低分辨率 resolution_low	12.000 Å
R 因子 r_factor	0.1900
R_work r_work	0.1900
R_free r_free	0.2260

fit	/app/data/saxs_computation/us/1usr/1usr.fit
pddf	/app/data/pr_computation/us/1usr/1usr.pr.out
profile	/app/data/saxs_computation/us/1usr/1usr.dat