SAXSdb — 1uzg

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1uzg
沉积日期 deposition_date	2004-03-11
结构标题 title	CRYSTAL STRUCTURE OF THE DENGUE TYPE 3 VIRUS ENVELOPE PROTEIN
关键词 keywords	VIRAL PROTEIN, MEMBRANE FUSION, FLAVIVIRUS, FUSION LOOP, CLASS 2 FUSION PROTEIN, GLYCOPROTEIN, ENVELOPE 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	42.86 Å
回转半径 Rg (电子) rg_electron	43.81 Å
零角强度 I(0) i0	120809000.00
分子量 molecular_weight	88548.0 kDa
排除体积 excluded_volume	110800 Å³
包络体积 envelope_volume	158280 Å³
水化壳体积 shell_volume	34820 Å³
包络直径 envelope_diameter	154.1 Å
壳层 Rg shell_rg	40.54 Å
包络 Rg envelope_rg	43.34 Å
形状 Rg shape_rg	43.79 Å
总 Rg total_rg	43.67 Å
总原子数 total_atoms	6200
残基数 n_residues	784
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	144.3 Å
Rg (实空间) rg_real	43.55 Å
Rg 误差 (实空间) rg_real_error	1.71 Å
I(0) (实空间) i0_real	1.2080e+08
I(0) 误差 (实空间) i0_real_error	2.3280e+06
Rg (倒空间) rg_reciprocal	42.87 Å
I(0) (倒空间) i0_reciprocal	120700000.0000
解质量估计 total_estimate	0.7337
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	31.2 Å
偏度 Skewness skewness	0.616
峰度 Kurtosis kurtosis	-0.399
角度范围 angular_range	— – 0.1850 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	7298000.0000
实空间数据点数 n_real_points	38
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.639; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.476; Smooth: 0.139

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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 (6)

Entity 1 polymer

描述 description	MAJOR ENVELOPE PROTEIN E
分子量 formula_weight	43170.4 kDa
来源方法 src_method	man
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	6214

MRCVGVGNRDFVEGLSGATWVDVVLEHGGCVTTMAKNKPTLDIELQKTEATQLATLRKLCIEGKITNITTDSRCPTQGEAILPEEQDQNYVCKHTYVDRGWGNGCGLFGKGSLVTCAKFQCLESIEGKIVQHENLKYTVIITVHTGDQHQVGNETQGVTAEITSQASTAEAILPEYGTLGLECSPRTGLDFNEMILLTMKDKAWMVHRQWFFDLPLPWTSGATTKTPTWNRKELLVTFKNAHAKKQEVVVLGSQEGAMHTALTGATEIQTSGGTSIFAGHLKCRLKMDKLKLKGMSYAMCLNTFVLKKEVSETQHGTILIKVEYKGEDAPCKIPFSTEDGQGKAHNGRLITANPVVTKKEEPVNIEAEPPFGESNIVIGIGDKALKINWYRK

来源 Source

来源生物 organism	DENGUE VIRUS TYPE 3
NCBI 分类编号 ncbi_taxonomy_id	11069
宿主生物 host_organism	DROSOPHILA MELANOGASTER

Entity 2 branched

描述 description	beta-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	367.3 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 3 branched

描述 description	;beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	1057.0 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 4 branched

描述 description	;alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	732.7 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 5 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 6 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	14

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6. 折叠分类 (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

结构域编号 domain_id	1uzgA01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	98 — Tick-borne Encephalitis virus Glycoprotein; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Tick-borne Encephalitis virus Glycoprotein, domain 1

结构域编号 domain_id	1uzgA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	67 — Viral Envelope Glycoprotein; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Viral Envelope Glycoprotein, domain 2

结构域编号 domain_id	1uzgA03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	387 — Viral Envelope Glycoprotein; domain 3
同源超家族 H-superfamily homologous superfamily	10 — Viral Envelope Glycoprotein, domain 3

结构域编号 domain_id	1uzgA04
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	350 —

结构域编号 domain_id	1uzgB01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	98 — Tick-borne Encephalitis virus Glycoprotein; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Tick-borne Encephalitis virus Glycoprotein, domain 1

结构域编号 domain_id	1uzgB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	67 — Viral Envelope Glycoprotein; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Viral Envelope Glycoprotein, domain 2

结构域编号 domain_id	1uzgB03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	387 — Viral Envelope Glycoprotein; domain 3
同源超家族 H-superfamily homologous superfamily	10 — Viral Envelope Glycoprotein, domain 3

结构域编号 domain_id	1uzgB04
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	350 —

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7. 引用文献 (2)

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晶胞边长 a length_a	52.855 Å
晶胞边长 b length_b	68.631 Å
晶胞边长 c length_c	270.180 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 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	3.500 Å
最低分辨率 resolution_low	20.990 Å
R 因子 r_factor	0.2860
R_work r_work	0.2840
R_free r_free	0.3240

fit	/app/data/saxs_computation/uz/1uzg/1uzg.fit
pddf	/app/data/pr_computation/uz/1uzg/1uzg.pr.out
profile	/app/data/saxs_computation/uz/1uzg/1uzg.dat

CRYSTAL STRUCTURE OF THE DENGUE TYPE 3 VIRUS ENVELOPE PROTEIN

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