SAXSdb — 1f4w

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1f4w
沉积日期 deposition_date	2000-06-10
结构标题 title	CRYSTAL STRUCTURE OF AN ANTI-CARBOHYDRATE ANTIBODY DIRECTED AGAINST VIBRIO CHOLERAE O1 IN COMPLEX WITH ANTIGEN
关键词 keywords	anti-carbohydrate antibody, 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	24.67 Å
回转半径 Rg (电子) rg_electron	23.68 Å
零角强度 I(0) i0	34367300.00
分子量 molecular_weight	44805.0 kDa
排除体积 excluded_volume	55801 Å³
包络体积 envelope_volume	68697 Å³
水化壳体积 shell_volume	24376 Å³
包络直径 envelope_diameter	74.9 Å
壳层 Rg shell_rg	30.58 Å
包络 Rg envelope_rg	23.36 Å
形状 Rg shape_rg	23.67 Å
总 Rg total_rg	24.52 Å
总原子数 total_atoms	3154
残基数 n_residues	426
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	74.2 Å
Rg (实空间) rg_real	24.60 Å
Rg 误差 (实空间) rg_real_error	0.47 Å
I(0) (实空间) i0_real	3.4370e+07
I(0) 误差 (实空间) i0_real_error	4.5520e+05
Rg (倒空间) rg_reciprocal	24.62 Å
I(0) (倒空间) i0_reciprocal	34370000.0000
解质量估计 total_estimate	0.9149
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	27.1 Å
偏度 Skewness skewness	0.215
峰度 Kurtosis kurtosis	-0.593
角度范围 angular_range	— – 0.3200 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	6641000.0000
实空间数据点数 n_real_points	64
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.983; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.950

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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	ANTIBODY S-20-4, FAB FRAGMENT, LIGHT CHAIN
分子量 formula_weight	22513.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	L
原子数 atom_count	3205

QAVVTQESALTTSPGETVTLTCRSSTGTVTTSNYANWVQEKPDHLFTGLIGATNNRAAGVPVRFSGSLIGGKAALTITGAQTEDEAIYFCALWYSGHWVFGGGTKLTVLGQPKSSPSVTLFPPSSEELETNKATLVCTITDFYPGVVTVDWKVDGTPVTQGMETTNPSKQSNNKYMASSYLTLTARAWERHSSYSCQVTHEGHTVEKSLS

Entity 2 polymer

描述 description	ANTIBODY S-20-4, FAB FRAGMENT, HEAVY CHAIN
分子量 formula_weight	23274.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	H

EVQLEESGGGLVTPGGSLRLSCAASGYVFSTYDMSWVRQTPEKRLEWVAFISSGGGRTSYPDTVKGRFTISRDDAKNTLYLQMSSLQSEDTAMYYCTRHFYAVLDYWGRGTTLTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVP

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	51

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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	d1f4wh1
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	d1f4wh2
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.1.1.2 — C1 set domains (antibody constant domain-like)

结构域编号 domain_id	d1f4wl1
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	d1f4wl2
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.1.1.2 — C1 set domains (antibody constant domain-like)

CATH v4.4 (4 domains)

结构域编号 domain_id	1f4wH01
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	1f4wH02
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	1f4wL01
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	1f4wL02
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	45.670 Å
晶胞边长 b length_b	113.320 Å
晶胞边长 c length_c	46.210 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	100.69 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	2

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	—

分辨率 resolution	2.300 Å
最低分辨率 resolution_low	10.000 Å
R 因子 r_factor	—
R_work r_work	0.1970
R_free r_free	0.2610

fit	/app/data/saxs_computation/f4/1f4w/1f4w.fit
pddf	/app/data/pr_computation/f4/1f4w/1f4w.pr.out
profile	/app/data/saxs_computation/f4/1f4w/1f4w.dat

CRYSTAL STRUCTURE OF AN ANTI-CARBOHYDRATE ANTIBODY DIRECTED AGAINST VIBRIO CHOLERAE O1 IN COMPLEX WITH ANTIGEN

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

Entity 2 polymer

聚合体 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)