SAXSdb — 1it9

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1it9
沉积日期 deposition_date	2002-01-11
结构标题 title	CRYSTAL STRUCTURE OF AN ANTIGEN-BINDING FRAGMENT FROM A HUMANIZED VERSION OF THE ANTI-HUMAN FAS ANTIBODY HFE7A
关键词 keywords	IMMUNOGLOBULIN, FAB, ANTI_FAS, AGONISTIC_ANTIBODY, APOPTOSIS, ANTIBODY_HUMANIZATION, 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	25.67 Å
回转半径 Rg (电子) rg_electron	24.73 Å
零角强度 I(0) i0	38269600.00
分子量 molecular_weight	47051.0 kDa
排除体积 excluded_volume	58474 Å³
包络体积 envelope_volume	73381 Å³
水化壳体积 shell_volume	25016 Å³
包络直径 envelope_diameter	82.5 Å
壳层 Rg shell_rg	31.67 Å
包络 Rg envelope_rg	24.24 Å
形状 Rg shape_rg	24.72 Å
总 Rg total_rg	25.54 Å
总原子数 total_atoms	3313
残基数 n_residues	433
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	78.5 Å
Rg (实空间) rg_real	25.63 Å
Rg 误差 (实空间) rg_real_error	0.42 Å
I(0) (实空间) i0_real	3.8270e+07
I(0) 误差 (实空间) i0_real_error	4.5740e+05
Rg (倒空间) rg_reciprocal	25.65 Å
I(0) (倒空间) i0_reciprocal	38270000.0000
解质量估计 total_estimate	0.9137
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	27.9 Å
偏度 Skewness skewness	0.232
峰度 Kurtosis kurtosis	-0.600
角度范围 angular_range	— – 0.3100 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	8044000.0000
实空间数据点数 n_real_points	63
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.977; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.948

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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	HUMANIZED ANTIBODY HFE7A, LIGHT CHAIN
分子量 formula_weight	23501.9 kDa
来源方法 src_method	man
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	3319

EIVLTQSPGTLSLSPGERATLSCKASQSVDYDGDSYMNWYQQKPGQAPRLLIYAASNLESGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQSNEDPRTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFN

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	mouse
NCBI 分类编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Chlorocebus aethiops

Entity 2 polymer

描述 description	HUMANIZED ANTIBODY HFE7A, HEAVY CHAIN
分子量 formula_weight	23593.3 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

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

QVQLVQSGAEVKKPGASVKVSCKASGYTFTSYWMQWVKQAPGQGLEWMGEIDPSDSYTNYNQKFKGKATLTVDTSTSTAYMELSSLRSEDTAVYYCARNRDYSNNWYFDVWGEGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKV

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	mouse
NCBI 分类编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Chlorocebus aethiops

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	6

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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	d1it9h1
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	d1it9h2
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	d1it9l1
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	d1it9l2
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	1it9H01
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	1it9H02
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	1it9L01
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	1it9L02
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 (3)

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晶胞边长 a length_a	54.365 Å
晶胞边长 b length_b	82.746 Å
晶胞边长 c length_c	104.934 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	4

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	2.800 Å
最低分辨率 resolution_low	30.000 Å
R 因子 r_factor	0.2020
R_work r_work	0.2020
R_free r_free	0.2800

fit	/app/data/saxs_computation/it/1it9/1it9.fit
pddf	/app/data/pr_computation/it/1it9/1it9.pr.out
profile	/app/data/saxs_computation/it/1it9/1it9.dat

CRYSTAL STRUCTURE OF AN ANTIGEN-BINDING FRAGMENT FROM A HUMANIZED VERSION OF THE ANTI-HUMAN FAS ANTIBODY HFE7A

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 polymer

聚合体 Polymer

来源 Source

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 (3)

8. 文件与曲线 (10)

Files (7)

Curves (3)