1l2g

Structure of a C-terminally truncated form of glycoprotein D from HSV-1

Method: X-RAY DIFFRACTION D_max: 164.4 Å Quality: REASONABLE

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	1l2g
沉积日期 deposition_date	2002-02-21
结构标题 title	Structure of a C-terminally truncated form of glycoprotein D from HSV-1
关键词 keywords	Ig fold, viral envelope glycoprotein, 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	57.69 Å
回转半径 Rg (电子) rg_electron	57.84 Å
零角强度 I(0) i0	629452000.00
分子量 molecular_weight	218090.0 kDa
排除体积 excluded_volume	274930 Å³
包络体积 envelope_volume	276860 Å³
水化壳体积 shell_volume	38850 Å³
包络直径 envelope_diameter	182.0 Å
壳层 Rg shell_rg	66.33 Å
包络 Rg envelope_rg	54.19 Å
形状 Rg shape_rg	57.83 Å
总 Rg total_rg	57.99 Å
总原子数 total_atoms	15376
残基数 n_residues	1936
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	164.4 Å
Rg (实空间) rg_real	58.01 Å
Rg 误差 (实空间) rg_real_error	2.19 Å
I(0) (实空间) i0_real	6.2950e+08
I(0) 误差 (实空间) i0_real_error	1.3850e+07
Rg (倒空间) rg_reciprocal	57.32 Å
I(0) (倒空间) i0_reciprocal	628700000.0000
解质量估计 total_estimate	0.5689
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	3
主峰位置 r_peak_primary	30.4 Å
偏度 Skewness skewness	0.038
峰度 Kurtosis kurtosis	-1.398
角度范围 angular_range	— – 0.1350 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	4309000.0000
实空间数据点数 n_real_points	28
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.041; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.268; Smooth: 0.000

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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 (2)

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6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1l2ga_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.1 — Immunoglobulin
家族 Family family	b.1.1.1 — V set domains (antibody variable domain-like)

结构域编号 domain_id	d1l2gb_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.1 — Immunoglobulin
家族 Family family	b.1.1.1 — V set domains (antibody variable domain-like)

结构域编号 domain_id	d1l2gc_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.1 — Immunoglobulin
家族 Family family	b.1.1.1 — V set domains (antibody variable domain-like)

结构域编号 domain_id	d1l2gd_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.1 — Immunoglobulin
家族 Family family	b.1.1.1 — V set domains (antibody variable domain-like)

CATH v4.4 (4 domains)

结构域编号 domain_id	1l2gA00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	70 — Distorted Sandwich
拓扑 Topology topology	230 — Glycoprotein D; Chain: A;
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1l2gB00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	70 — Distorted Sandwich
拓扑 Topology topology	230 — Glycoprotein D; Chain: A;
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1l2gC00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	70 — Distorted Sandwich
拓扑 Topology topology	230 — Glycoprotein D; Chain: A;
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1l2gD00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	70 — Distorted Sandwich
拓扑 Topology topology	230 — Glycoprotein D; Chain: A;
同源超家族 H-superfamily homologous superfamily	10 —

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7. 引用文献 (2)

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晶胞边长 a length_a	131.416 Å
晶胞边长 b length_b	131.416 Å
晶胞边长 c length_c	83.265 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	16

空间群 space_group	P 4
空间群编号 int_tables_number	75
晶系 crystal_system	—

分辨率 resolution	2.850 Å
最低分辨率 resolution_low	30.000 Å
R 因子 r_factor	0.2830
R_work r_work	0.2780
R_free r_free	0.2970

描述 description	Glycoprotein D
分子量 formula_weight	31837.2 kDa
来源方法 src_method	man
拷贝数 entity_count	4

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,D,C
原子数 atom_count	15376

Structure of a C-terminally truncated form of glycoprotein D from HSV-1

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 (2)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 non-polymer

6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. 引用文献 (2)

8. 文件与曲线 (10)

Files (7)

Curves (3)

来源生物 organism	Human herpesvirus 1
通用名 common_name	Herpes simplex virus type 1
NCBI 分类编号 ncbi_taxonomy_id	10298
宿主生物 host_organism	Spodoptera frugiperda

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	4

fit	/app/data/saxs_computation/l2/1l2g/1l2g.fit
pddf	/app/data/pr_computation/l2/1l2g/1l2g.pr.out
profile	/app/data/saxs_computation/l2/1l2g/1l2g.dat