SAXSdb — 1ggq

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1ggq
沉积日期 deposition_date	2000-09-14
结构标题 title	OUTER SURFACE PROTEIN C (OSPC) OF BORRELIA BURGDORFERI STRAIN B31
关键词 keywords	Lyme disease antigen, helical bundle, homodimer, MEMBRANE PROTEIN; MEMBRANE 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	34.37 Å
回转半径 Rg (电子) rg_electron	35.19 Å
零角强度 I(0) i0	73818400.00
分子量 molecular_weight	69131.0 kDa
排除体积 excluded_volume	87155 Å³
包络体积 envelope_volume	110350 Å³
水化壳体积 shell_volume	28815 Å³
包络直径 envelope_diameter	138.0 Å
壳层 Rg shell_rg	36.62 Å
包络 Rg envelope_rg	36.22 Å
形状 Rg shape_rg	35.13 Å
总 Rg total_rg	35.51 Å
总原子数 total_atoms	4847
残基数 n_residues	648
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	129.2 Å
Rg (实空间) rg_real	34.93 Å
Rg 误差 (实空间) rg_real_error	1.61 Å
I(0) (实空间) i0_real	7.3820e+07
I(0) 误差 (实空间) i0_real_error	1.2600e+06
Rg (倒空间) rg_reciprocal	34.58 Å
I(0) (倒空间) i0_reciprocal	73800000.0000
解质量估计 total_estimate	0.7475
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	30.9 Å
偏度 Skewness skewness	0.733
峰度 Kurtosis kurtosis	0.058
角度范围 angular_range	— – 0.2300 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	8430000.0000
实空间数据点数 n_real_points	47
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.471; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.442; Smooth: 0.858

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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	OUTER SURFACE PROTEIN C
分子量 formula_weight	18597.4 kDa
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	4959

MKGPNLTEISKKITDSNAVLLAVKEVEALLSSIDEIAAKAIGKKIHQNNGLDTENNHNGSLLAGAYAISTLIKQKLDGLKNEGLKEKIDAAKKCSETFTNKLKEKHTDLGKEGVTDADAKEAILKTNGTKTKGAEELGKLFESVEVLSKAAKEMLANSVKELTSPVVAESPKKP

来源 Source

来源生物 organism	Borrelia burgdorferi
NCBI 分类编号 ncbi_taxonomy_id	224326
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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	112

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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	d1ggqa_
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.24.12.1 — Outer surface protein C (OspC)

结构域编号 domain_id	d1ggqb_
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.24.12.1 — Outer surface protein C (OspC)

结构域编号 domain_id	d1ggqc_
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.24.12.1 — Outer surface protein C (OspC)

结构域编号 domain_id	d1ggqd_
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.24.12.1 — Outer surface protein C (OspC)

CATH v4.4 (4 domains)

结构域编号 domain_id	1ggqA00
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	1ggqB00
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	1ggqC00
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	1ggqD00
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 (1)

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晶胞边长 a length_a	127.206 Å
晶胞边长 b length_b	33.654 Å
晶胞边长 c length_c	47.993 Å
晶胞夹角 α angle_alpha	84.04 °
晶胞夹角 β angle_beta	81.55 °
晶胞夹角 γ angle_gamma	89.23 °
晶胞分子数 Z z_pdb	4

空间群 space_group	P 1
空间群编号 int_tables_number	1
晶系 crystal_system	—

分辨率 resolution	2.510 Å
最低分辨率 resolution_low	40.740 Å
R 因子 r_factor	0.2310
R_work r_work	0.2310
R_free r_free	0.2650

fit	/app/data/saxs_computation/gg/1ggq/1ggq.fit
pddf	/app/data/pr_computation/gg/1ggq/1ggq.pr.out
profile	/app/data/saxs_computation/gg/1ggq/1ggq.dat

OUTER SURFACE PROTEIN C (OSPC) OF BORRELIA BURGDORFERI STRAIN B31

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 (3)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 non-polymer

Entity 3 water

6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)