SAXSdb — 1vsg

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1vsg
沉积日期 deposition_date	1990-10-22
结构标题 title	2.9 ANGSTROMS RESOLUTION STRUCTURE OF THE N-TERMINAL DOMAIN OF A VARIANT SURFACE GLYCOPROTEIN FROM TRYPANOSOMA BRUCEI
关键词 keywords	GLYCOPROTEIN; GLYCOPROTEIN
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	33.05 Å
回转半径 Rg (电子) rg_electron	32.58 Å
零角强度 I(0) i0	100142000.00
分子量 molecular_weight	78194.0 kDa
排除体积 excluded_volume	97330 Å³
包络体积 envelope_volume	119000 Å³
水化壳体积 shell_volume	32074 Å³
包络直径 envelope_diameter	105.1 Å
壳层 Rg shell_rg	37.62 Å
包络 Rg envelope_rg	32.30 Å
形状 Rg shape_rg	32.57 Å
总 Rg total_rg	32.99 Å
总原子数 total_atoms	5490
残基数 n_residues	724
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	105.7 Å
Rg (实空间) rg_real	33.35 Å
Rg 误差 (实空间) rg_real_error	0.76 Å
I(0) (实空间) i0_real	1.0010e+08
I(0) 误差 (实空间) i0_real_error	1.4790e+06
Rg (倒空间) rg_reciprocal	33.23 Å
I(0) (倒空间) i0_reciprocal	100100000.0000
解质量估计 total_estimate	0.8321
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	28.6 Å
偏度 Skewness skewness	0.412
峰度 Kurtosis kurtosis	-0.771
角度范围 angular_range	— – 0.2400 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	22050000.0000
实空间数据点数 n_real_points	49
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.731; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.745; Smooth: 0.875

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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 (4)

Entity 1 polymer

描述 description	VARIANT SURFACE GLYCOPROTEIN MITAT 1.2
分子量 formula_weight	38844.7 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	5508

AAEKGFKQAFWQPLCQVSEELDDQPKGALFTLQAAASKIQKMRDAALRASIYAEINHGTNRAKAAVIVANHYAMKADSGLEALKQTLSSQEVTATATASYLKGRIDEYLNLLLQTKESGTSGCMMDTSGTNTVTKAGGTIGGVPCKLQLSPIQPKRPAATYLGKAGYVGLTRQADAANNFHDNDAECRLASGHNTNGLGKSGQLSAAVTMAAGYVTVANSQTAVTVQALDALQEASGAAHQPWIDAWKAKKALTGAETAEFRNETAGIAGKTGVTKLVEEALLKKKDSEASEIQTELKKYFSGHENEQWTAIEKLISEQPVAQNLVGDNQPTKLGELEGNAKLTTILAYYRMETAGKFEVLTQK

来源 Source

来源生物 organism	Trypanosoma brucei brucei
NCBI 分类编号 ncbi_taxonomy_id	5702

Entity 2 branched

描述 description	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	586.5 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 3 branched

描述 description	alpha-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	586.5 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 4 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	18

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6. 折叠分类 (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d1vsga_
类 Class class	h — Coiled coil proteins
折叠类型 Fold fold	h.4 — Antiparallel coiled-coil
超家族 Superfamily superfamily	h.4.1 — Variant surface glycoprotein (N-terminal domain)
家族 Family family	h.4.1.1 — Variant surface glycoprotein (N-terminal domain)

结构域编号 domain_id	d1vsgb_
类 Class class	h — Coiled coil proteins
折叠类型 Fold fold	h.4 — Antiparallel coiled-coil
超家族 Superfamily superfamily	h.4.1 — Variant surface glycoprotein (N-terminal domain)
家族 Family family	h.4.1.1 — Variant surface glycoprotein (N-terminal domain)

CATH v4.4 (4 domains)

结构域编号 domain_id	1vsgA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	150 — Variant Surface Glycoprotein; Chain A domain 1
同源超家族 H-superfamily homologous superfamily	10 — Variant Surface Glycoprotein, subunit A domain 1

结构域编号 domain_id	1vsgA02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	470 — Variant Surface Glycoprotein, subunit A; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Variant Surface Glycoprotein, subunit A, domain 2

结构域编号 domain_id	1vsgB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	150 — Variant Surface Glycoprotein; Chain A domain 1
同源超家族 H-superfamily homologous superfamily	10 — Variant Surface Glycoprotein, subunit A domain 1

结构域编号 domain_id	1vsgB02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	470 — Variant Surface Glycoprotein, subunit A; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Variant Surface Glycoprotein, subunit A, domain 2

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7. 引用文献 (3)

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晶胞边长 a length_a	95.500 Å
晶胞边长 b length_b	97.500 Å
晶胞边长 c length_c	123.700 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	2.900 Å
最低分辨率 resolution_low	— Å
R 因子 r_factor	—
R_work r_work	0.2200
R_free r_free	—

fit	/app/data/saxs_computation/vs/1vsg/1vsg.fit
pddf	/app/data/pr_computation/vs/1vsg/1vsg.pr.out
profile	/app/data/saxs_computation/vs/1vsg/1vsg.dat

2.9 ANGSTROMS RESOLUTION STRUCTURE OF THE N-TERMINAL DOMAIN OF A VARIANT SURFACE GLYCOPROTEIN FROM TRYPANOSOMA BRUCEI

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution