1xcq

Complex HCV core-Fab 19D9D6-Protein L mutant (D55A,L57H,Y64W) in space group P21

Method: X-RAY DIFFRACTION D_max: 194.3 Å Quality: GOOD

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

下载 Download SAXS (.dat) P(r) (.pr.out) CIF

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1xcq
沉积日期 deposition_date	2004-09-03
结构标题 title	Complex HCV core-Fab 19D9D6-Protein L mutant (D55A,L57H,Y64W) in space group P21
关键词 keywords	Crystal packing, Fab, protein L, Peptide complex, 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	56.37 Å
回转半径 Rg (电子) rg_electron	56.24 Å
零角强度 I(0) i0	788004000.00
分子量 molecular_weight	231130.0 kDa
排除体积 excluded_volume	288090 Å³
包络体积 envelope_volume	478440 Å³
水化壳体积 shell_volume	74638 Å³
包络直径 envelope_diameter	198.7 Å
壳层 Rg shell_rg	55.05 Å
包络 Rg envelope_rg	54.12 Å
形状 Rg shape_rg	56.19 Å
总 Rg total_rg	56.37 Å
总原子数 total_atoms	16281
残基数 n_residues	2117
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	194.3 Å
Rg (实空间) rg_real	56.54 Å
Rg 误差 (实空间) rg_real_error	2.54 Å
I(0) (实空间) i0_real	7.8800e+08
I(0) 误差 (实空间) i0_real_error	1.7930e+07
Rg (倒空间) rg_reciprocal	56.21 Å
I(0) (倒空间) i0_reciprocal	787600000.0000
解质量估计 total_estimate	0.8441
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	76.3 Å
偏度 Skewness skewness	0.347
峰度 Kurtosis kurtosis	-0.240
角度范围 angular_range	— – 0.1400 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	30850000.0000
实空间数据点数 n_real_points	29
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.813; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.970; Smooth: 0.560

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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 (5)

Entity 1 polymer

描述 description	Capsid protein C
分子量 formula_weight	4909.7 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	P,Q,S
原子数 atom_count	16467

STNPKPQRKTKRNTNRRPQDVKFPGGGQIVGGVYLLPRRGPRLG

Entity 2 polymer

描述 description	Monoclonal antibody 19D9D6 Light chain
分子量 formula_weight	24334.1 kDa
来源方法 src_method	nat
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,C,E,G

DIVMSQSPSSLAVSAGEKVTMSCKSSQSLLNSRTRKNYLAWYQQKPGQSPKVLIYWASTRESGVPDRFTGRGSGTDFTLTISSVQAEDQAVYYCKQAYIPPLTFGAGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Entity 3 polymer

描述 description	Monoclonal antibody 19D9D6 Heavy chain
分子量 formula_weight	23563.4 kDa
来源方法 src_method	nat
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B,D,F,H

QIQLVQSGPELKKPGETVKISCKASGYTFTDFSMHWVNQAPGKGLNWMGWVNTETGEPTYADDFKGRFAFSLETSASTAYLQINSLKNEDTATYFCARFLLRQYFDVWGAGTTVTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR

Entity 4 polymer

描述 description	Protein L
分子量 formula_weight	8903.0 kDa
突变 mutation	D55A,L57H,Y64W
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	L,M,N,O

MNIKFAGKEKTPEEPKEEVTIKVNLIFADGKIQTAEFKGTFEEATAEAYRYAALHAKVNGEWTADLEDGGNHMNIKFAGK

来源 Source

来源生物 organism	Finegoldia magna
NCBI 分类编号 ncbi_taxonomy_id	334413
宿主生物 host_organism	Escherichia coli

Entity 5 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	186

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6. 折叠分类 (SCOP + CATH) 20 domains

CATH v4.4 (20 domains)

结构域编号 domain_id	1xcqA01
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	1xcqA02
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	1xcqB01
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	1xcqB02
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	1xcqC01
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	1xcqC02
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	1xcqD01
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	1xcqD02
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	1xcqE01
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	1xcqE02
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	1xcqF01
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	1xcqF02
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	1xcqG01
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	1xcqG02
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	1xcqH01
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	1xcqH02
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	1xcqL00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	20 — Ubiquitin-like (UB roll)
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1xcqM00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	20 — Ubiquitin-like (UB roll)
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1xcqN00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	20 — Ubiquitin-like (UB roll)
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1xcqO00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	20 — Ubiquitin-like (UB roll)
同源超家族 H-superfamily homologous superfamily	10 —

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7. 引用文献 (1)

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晶胞边长 a length_a	43.603 Å
晶胞边长 b length_b	230.522 Å
晶胞边长 c length_c	123.645 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	91.67 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

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	3.500 Å
最低分辨率 resolution_low	21.620 Å
R 因子 r_factor	0.1952
R_work r_work	0.1916
R_free r_free	0.2638

fit	/app/data/saxs_computation/xc/1xcq/1xcq.fit
pddf	/app/data/pr_computation/xc/1xcq/1xcq.pr.out
profile	/app/data/saxs_computation/xc/1xcq/1xcq.dat

Complex HCV core-Fab 19D9D6-Protein L mutant (D55A,L57H,Y64W) in space group P21

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 (5)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

Entity 3 polymer

聚合体 Polymer

Entity 4 polymer

聚合体 Polymer

来源 Source

Entity 5 water

6. 折叠分类 (SCOP + CATH) 20 domains

CATH v4.4 (20 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)