2ga0

Variable Small Protein 1 of Borrelia turicatae (VspA or Vsp1)

Method: X-RAY DIFFRACTION D_max: 148.0 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	2ga0
沉积日期 deposition_date	2006-03-07
结构标题 title	Variable Small Protein 1 of Borrelia turicatae (VspA or Vsp1)
关键词 keywords	helical bundle, Ni(II) binding sites, IMMUNE SYSTEM; IMMUNE SYSTEM
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	40.65 Å
回转半径 Rg (电子) rg_electron	40.77 Å
零角强度 I(0) i0	264884000.00
分子量 molecular_weight	135530.0 kDa
排除体积 excluded_volume	171660 Å³
包络体积 envelope_volume	229400 Å³
水化壳体积 shell_volume	50365 Å³
包络直径 envelope_diameter	146.9 Å
壳层 Rg shell_rg	42.61 Å
包络 Rg envelope_rg	40.71 Å
形状 Rg shape_rg	40.76 Å
总 Rg total_rg	40.91 Å
总原子数 total_atoms	9470
残基数 n_residues	1312
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	148.0 Å
Rg (实空间) rg_real	40.91 Å
Rg 误差 (实空间) rg_real_error	1.94 Å
I(0) (实空间) i0_real	2.6490e+08
I(0) 误差 (实空间) i0_real_error	5.2140e+06
Rg (倒空间) rg_reciprocal	40.65 Å
I(0) (倒空间) i0_reciprocal	264800000.0000
解质量估计 total_estimate	0.8247
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	45.5 Å
偏度 Skewness skewness	0.579
峰度 Kurtosis kurtosis	0.018
角度范围 angular_range	— – 0.1950 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	22310000.0000
实空间数据点数 n_real_points	40
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.696; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.791; Smooth: 0.837

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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 (3)

Entity 1 polymer

描述 description	surface protein VspA
分子量 formula_weight	18501.0 kDa
来源方法 src_method	man
拷贝数 entity_count	8

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F,G,H
原子数 atom_count	9606

SDGTVIDLATITKNITDAVAFAKSVKDVHTLVKSIDELAKAIGKKIGANGLETDADKNAKLISGAYSVISAVDTKLASLEKKVGISDDLKGKITTVKNASTSFLTKAKSKTADLGKDDVKDADAKTAIDIADTGAKDKGAEELIKLNTAIDALLTSAEAAVTAAINALSTPAKSASTVQSN

来源 Source

来源生物 organism	Borrelia turicatae
NCBI 分类编号 ncbi_taxonomy_id	142
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

描述 description	NICKEL (II) ION
分子量 formula_weight	58.7 kDa
来源方法 src_method	syn
拷贝数 entity_count	14

Entity 3 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	136

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6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d2ga0a_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.24 — Four-helical up-and-down bundle
超家族 Superfamily superfamily	a.24.12 — Outer surface protein C (OspC)
家族 Family family	a.24.12.0 — automated matches

结构域编号 domain_id	d2ga0b_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.24 — Four-helical up-and-down bundle
超家族 Superfamily superfamily	a.24.12 — Outer surface protein C (OspC)
家族 Family family	a.24.12.0 — automated matches

结构域编号 domain_id	d2ga0c_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.24 — Four-helical up-and-down bundle
超家族 Superfamily superfamily	a.24.12 — Outer surface protein C (OspC)
家族 Family family	a.24.12.0 — automated matches

结构域编号 domain_id	d2ga0d_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.24 — Four-helical up-and-down bundle
超家族 Superfamily superfamily	a.24.12 — Outer surface protein C (OspC)
家族 Family family	a.24.12.0 — automated matches

结构域编号 domain_id	d2ga0e_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.24 — Four-helical up-and-down bundle
超家族 Superfamily superfamily	a.24.12 — Outer surface protein C (OspC)
家族 Family family	a.24.12.0 — automated matches

结构域编号 domain_id	d2ga0f_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.24 — Four-helical up-and-down bundle
超家族 Superfamily superfamily	a.24.12 — Outer surface protein C (OspC)
家族 Family family	a.24.12.0 — automated matches

结构域编号 domain_id	d2ga0g_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.24 — Four-helical up-and-down bundle
超家族 Superfamily superfamily	a.24.12 — Outer surface protein C (OspC)
家族 Family family	a.24.12.0 — automated matches

结构域编号 domain_id	d2ga0h_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.24 — Four-helical up-and-down bundle
超家族 Superfamily superfamily	a.24.12 — Outer surface protein C (OspC)
家族 Family family	a.24.12.0 — automated matches

CATH v4.4 (8 domains)

结构域编号 domain_id	2ga0A00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
同源超家族 H-superfamily homologous superfamily	240 — Lipoprotein, type 6

结构域编号 domain_id	2ga0B00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
同源超家族 H-superfamily homologous superfamily	240 — Lipoprotein, type 6

结构域编号 domain_id	2ga0C00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
同源超家族 H-superfamily homologous superfamily	240 — Lipoprotein, type 6

结构域编号 domain_id	2ga0D00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
同源超家族 H-superfamily homologous superfamily	240 — Lipoprotein, type 6

结构域编号 domain_id	2ga0E00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
同源超家族 H-superfamily homologous superfamily	240 — Lipoprotein, type 6

结构域编号 domain_id	2ga0F00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
同源超家族 H-superfamily homologous superfamily	240 — Lipoprotein, type 6

结构域编号 domain_id	2ga0G00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
同源超家族 H-superfamily homologous superfamily	240 — Lipoprotein, type 6

结构域编号 domain_id	2ga0H00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
同源超家族 H-superfamily homologous superfamily	240 — Lipoprotein, type 6

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7. 引用文献 (2)

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晶胞边长 a length_a	241.835 Å
晶胞边长 b length_b	69.105 Å
晶胞边长 c length_c	87.578 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	104.95 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	32

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	—

分辨率 resolution	2.700 Å
最低分辨率 resolution_low	50.000 Å
R 因子 r_factor	0.2190
R_work r_work	0.2160
R_free r_free	0.2720

fit	/app/data/saxs_computation/ga/2ga0/2ga0.fit
pddf	/app/data/pr_computation/ga/2ga0/2ga0.pr.out
profile	/app/data/saxs_computation/ga/2ga0/2ga0.dat