SAXSdb — 8ee2

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8ee2
沉积日期 deposition_date	2022-09-06
结构标题 title	Crystal Structure of Nanobody VHH219 Bound to Its Antigen PA14 Cif
关键词 keywords	Pseudomonas aeruginosa, nanobody VHH, immunoglobulin domain, CFTR inhibitory factor (Cif), 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	40.33 Å
回转半径 Rg (电子) rg_electron	39.38 Å
零角强度 I(0) i0	1071260000.00
分子量 molecular_weight	269950.0 kDa
排除体积 excluded_volume	337340 Å³
包络体积 envelope_volume	425060 Å³
水化壳体积 shell_volume	83721 Å³
包络直径 envelope_diameter	132.0 Å
壳层 Rg shell_rg	49.30 Å
包络 Rg envelope_rg	39.12 Å
形状 Rg shape_rg	39.30 Å
总 Rg total_rg	40.11 Å
总原子数 total_atoms	19052
残基数 n_residues	2414
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	123.1 Å
Rg (实空间) rg_real	40.08 Å
Rg 误差 (实空间) rg_real_error	0.59 Å
I(0) (实空间) i0_real	1.0710e+09
I(0) 误差 (实空间) i0_real_error	1.7580e+07
Rg (倒空间) rg_reciprocal	40.33 Å
I(0) (倒空间) i0_reciprocal	1072000000.0000
解质量估计 total_estimate	0.8941
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	53.7 Å
偏度 Skewness skewness	0.054
峰度 Kurtosis kurtosis	-0.514
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	144700000.0000
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: 0.908; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.962; Smooth: 0.933

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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	CFTR inhibitory factor
分子量 formula_weight	34164.7 kDa
来源方法 src_method	man
拷贝数 entity_count	6

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,E,F,I,J
原子数 atom_count	19194

AEEFPVPNGFESAYREVDGVKLHYVKGGQGPLVMLVHGFGQTWYEWHQLMPELAKRFTVIAPDLPGLGQSEPPKTGYSGEQVAVYLHKLARQFSPDRPFDLVAHDIGIWNTYPMVVKNQADIARLVYMEAPIPDARIYRFPAFTAQGESLVWHFSFFAADDRLAETLIAGKERFFLEHFIKSHASNTEVFSERLLDLYARSYAKPHSLNASFEYYRALNESVRQNAELAKTRLQMPTMTLAGGGHGGMGTFQLEQMKAYAEDVEGHVLPGCGHWLPEECAAPMNRLVIDFLSRGRHHHHHH

来源 Source

来源生物 organism	Pseudomonas aeruginosa PA14
NCBI 分类编号 ncbi_taxonomy_id	652611
宿主生物 host_organism	Escherichia coli

Entity 2 polymer

描述 description	Nanobody VHH219
分子量 formula_weight	13629.1 kDa
来源方法 src_method	man
拷贝数 entity_count	6

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	C,D,G,H,K,L

MAEVQLVESGGGLVQPGGSLRLSCTTSTSLFSITTMGWYRQAPGKQRELVASIKRGGGTNYADSMKGRFTISRDNARNTVFLEMNNLTTEDTAVYYCNAAILAYTGEVTNYWGQGTQVTVSSGQAGQ

来源 Source

来源生物 organism	Vicugna pacos
NCBI 分类编号 ncbi_taxonomy_id	30538
宿主生物 host_organism	Escherichia coli BL21

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	108

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6. 折叠分类 (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

结构域编号 domain_id	8ee2A01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

结构域编号 domain_id	8ee2B01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

结构域编号 domain_id	8ee2C01
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	8ee2D01
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	8ee2E01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

结构域编号 domain_id	8ee2F01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

结构域编号 domain_id	8ee2G01
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	8ee2H01
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	8ee2I01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

结构域编号 domain_id	8ee2J01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

结构域编号 domain_id	8ee2K01
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	8ee2L01
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	76.204 Å
晶胞边长 b length_b	162.599 Å
晶胞边长 c length_c	106.255 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	95.36 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	12

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

分辨率 resolution	2.400 Å
最低分辨率 resolution_low	43.750 Å
R 因子 r_factor	0.1967
R_work r_work	0.1951
R_free r_free	0.2274

fit	/app/data/saxs_computation/ee/8ee2/8ee2.fit
pddf	/app/data/pr_computation/ee/8ee2/8ee2.pr.out
profile	/app/data/saxs_computation/ee/8ee2/8ee2.dat

Crystal Structure of Nanobody VHH219 Bound to Its Antigen PA14 Cif

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) 12 domains

CATH v4.4 (12 domains)

7. 引用文献 (3)

8. 文件与曲线 (10)

Files (7)

Curves (3)