SAXSdb — 1h8o

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1h8o
沉积日期 deposition_date	2001-02-14
结构标题 title	Three-dimensional structure of anti-ampicillin single chain Fv fragment.
关键词 keywords	ANTIBODY, FV FRAGMENT, ANTI-AMPICILLIN; ANTIBODY
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	27.38 Å
回转半径 Rg (电子) rg_electron	27.09 Å
零角强度 I(0) i0	39887300.00
分子量 molecular_weight	48358.0 kDa
排除体积 excluded_volume	60204 Å³
包络体积 envelope_volume	76870 Å³
水化壳体积 shell_volume	25282 Å³
包络直径 envelope_diameter	97.7 Å
壳层 Rg shell_rg	32.31 Å
包络 Rg envelope_rg	26.87 Å
形状 Rg shape_rg	27.09 Å
总 Rg total_rg	27.67 Å
总原子数 total_atoms	3410
残基数 n_residues	440
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	93.1 Å
Rg (实空间) rg_real	27.59 Å
Rg 误差 (实空间) rg_real_error	0.74 Å
I(0) (实空间) i0_real	3.9890e+07
I(0) 误差 (实空间) i0_real_error	6.0450e+05
Rg (倒空间) rg_reciprocal	27.52 Å
I(0) (倒空间) i0_reciprocal	39890000.0000
解质量估计 total_estimate	0.8540
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	27.3 Å
偏度 Skewness skewness	0.517
峰度 Kurtosis kurtosis	-0.297
角度范围 angular_range	— – 0.2900 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	6834000.0000
实空间数据点数 n_real_points	59
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.773; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.890; Smooth: 0.888

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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	MUTANT AL2 6E7P9G
分子量 formula_weight	27006.7 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	3520

DYKDIVLTQSHKFMSTSVGDRVSITCKASQDVGTAVAWYQQKPGQSPKLLIYWASTRHTGVPDRFTGSGSGTDFTLTISNVQSEDLADYFCQQYSSYPLTFGAGTKLELKRGGGGSGGGGSGGGGSGGGGSQVQLQEPGGELVRPGASVKLSCKASGYTFTSYWINWVKQRPGQGLEWIGNIYPSDSYTNYNQKFKDKATLTVDKSSSTAYMQLSSLTSEDSAVYFCARWGYWGQGTLVTVSAASGAHHHHH

来源 Source

来源生物 organism	MUS MUSCULUS
NCBI 分类编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	ESCHERICHIA COLI K-12

Entity 2 non-polymer

描述 description	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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	110

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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	d1h8oa1
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	d1h8oa2
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	d1h8ob1
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	d1h8ob2
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	1h8oA01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

结构域编号 domain_id	1h8oA02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

结构域编号 domain_id	1h8oB01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

结构域编号 domain_id	1h8oB02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

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7. 引用文献 (1)

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晶胞边长 a length_a	59.690 Å
晶胞边长 b length_b	89.850 Å
晶胞边长 c length_c	97.260 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	2.750 Å
最低分辨率 resolution_low	11.940 Å
R 因子 r_factor	0.1780
R_work r_work	0.1780
R_free r_free	0.2580

fit	/app/data/saxs_computation/h8/1h8o/1h8o.fit
pddf	/app/data/pr_computation/h8/1h8o/1h8o.pr.out
profile	/app/data/saxs_computation/h8/1h8o/1h8o.dat

Three-dimensional structure of anti-ampicillin single chain Fv fragment.

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