2bf1

Structure of an unliganded and fully-glycosylated SIV gp120 envelope glycoprotein

Method: X-RAY DIFFRACTION D_max: 82.2 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	2bf1
沉积日期 deposition_date	2004-12-02
结构标题 title	Structure of an unliganded and fully-glycosylated SIV gp120 envelope glycoprotein
关键词 keywords	VIRUS PROTEIN, SIV, GP120, ENVELOPE GLYCOPROTEIN, AIDS, COAT PROTEIN; VIRUS 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	24.17 Å
回转半径 Rg (电子) rg_electron	22.92 Å
零角强度 I(0) i0	36148700.00
分子量 molecular_weight	44248.0 kDa
排除体积 excluded_volume	54796 Å³
包络体积 envelope_volume	78371 Å³
水化壳体积 shell_volume	28143 Å³
包络直径 envelope_diameter	86.3 Å
壳层 Rg shell_rg	30.33 Å
包络 Rg envelope_rg	23.29 Å
形状 Rg shape_rg	22.84 Å
总 Rg total_rg	24.15 Å
总原子数 total_atoms	3085
残基数 n_residues	304
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	82.2 Å
Rg (实空间) rg_real	24.07 Å
Rg 误差 (实空间) rg_real_error	0.57 Å
I(0) (实空间) i0_real	3.6150e+07
I(0) 误差 (实空间) i0_real_error	4.7990e+05
Rg (倒空间) rg_reciprocal	24.09 Å
I(0) (倒空间) i0_reciprocal	36150000.0000
解质量估计 total_estimate	0.7851
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	3
主峰位置 r_peak_primary	30.8 Å
偏度 Skewness skewness	0.287
峰度 Kurtosis kurtosis	-0.139
角度范围 angular_range	— – 0.3300 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	14860000.0000
实空间数据点数 n_real_points	65
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.734; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; 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 (9)

Entity 1 polymer

描述 description	EXTERIOR MEMBRANE GLYCOPROTEIN GP120
分子量 formula_weight	36833.7 kDa
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	3085

HMELALNVTESFDAWENTVTEQAIEDVWQLFETSIKPCVKLSPLCIGAGHCNTSIIQESCDKHYWDTIRFRYCAPPGYALLRCNDTNYSGFMPKCSKVVVSSCTRMMETQTSTWFGFNGTRAENRTYIYWHGRDNRTIISLNKYYNLTMKCRGAGWCWFGGNWKDAIKEMKQTIVKHPRYTGTNNTDKINLTAPRGGDPEVTFMWTNCRGEFLYCKMNWFLNWVEDRDVTNQRPKERHRRNYVPCHIRQIINTWHKVGKNVYLPPREGDLTCNSTVTSLIANIDWTDGNQTNITMSAEVAELYRLELGDYKLVEIT

来源 Source

来源生物 organism	SIMIAN IMMUNODEFICIENCY VIRUS
通用名 common_name	SIV
NCBI 分类编号 ncbi_taxonomy_id	11723
宿主生物 host_organism	TRICHOPLUSIA NI

Entity 2 branched

描述 description	;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-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	3

Entity 3 branched

描述 description	;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-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	2

Entity 4 branched

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	570.5 kDa
来源方法 src_method	man
拷贝数 entity_count	2

Entity 5 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 6 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 7 branched

描述 description	;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	910.8 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 8 branched

描述 description	;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	748.7 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 9 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	2

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6. 折叠分类 (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

结构域编号 domain_id	2bf1A00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	170 — Beta Complex
拓扑 Topology topology	40 — HIV Envelope Protein Gp120; Chain G
同源超家族 H-superfamily homologous superfamily	20 — Human immunodeficiency virus 1, Gp160, envelope glycoprotein

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7. 引用文献 (2)

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晶胞边长 a length_a	108.048 Å
晶胞边长 b length_b	108.048 Å
晶胞边长 c length_c	117.701 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 43 21 2
空间群编号 int_tables_number	96
晶系 crystal_system	—

分辨率 resolution	4.000 Å
最低分辨率 resolution_low	26.000 Å
R 因子 r_factor	0.3850
R_work r_work	0.3850
R_free r_free	0.3880

fit	/app/data/saxs_computation/bf/2bf1/2bf1.fit
pddf	/app/data/pr_computation/bf/2bf1/2bf1.pr.out
profile	/app/data/saxs_computation/bf/2bf1/2bf1.dat