SAXSdb — 1igc

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1igc
沉积日期 deposition_date	1994-08-05
结构标题 title	IGG1 FAB FRAGMENT (MOPC21) COMPLEX WITH DOMAIN III OF PROTEIN G FROM STREPTOCOCCUS
关键词 keywords	PROTEIN G, STREPTOCOCCUS, COMPLEX (ANTIBODY-BINDING PROTEIN) COMPLEX; COMPLEX (ANTIBODY/BINDING PROTEIN)
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	25.98 Å
回转半径 Rg (电子) rg_electron	24.97 Å
零角强度 I(0) i0	49994200.00
分子量 molecular_weight	53655.0 kDa
排除体积 excluded_volume	66547 Å³
包络体积 envelope_volume	81667 Å³
水化壳体积 shell_volume	27154 Å³
包络直径 envelope_diameter	77.3 Å
壳层 Rg shell_rg	32.35 Å
包络 Rg envelope_rg	24.67 Å
形状 Rg shape_rg	24.96 Å
总 Rg total_rg	25.80 Å
总原子数 total_atoms	3772
残基数 n_residues	493
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	79.8 Å
Rg (实空间) rg_real	25.90 Å
Rg 误差 (实空间) rg_real_error	0.54 Å
I(0) (实空间) i0_real	4.9990e+07
I(0) 误差 (实空间) i0_real_error	7.0010e+05
Rg (倒空间) rg_reciprocal	25.93 Å
I(0) (倒空间) i0_reciprocal	50000000.0000
解质量估计 total_estimate	0.9134
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	31.4 Å
偏度 Skewness skewness	0.176
峰度 Kurtosis kurtosis	-0.621
角度范围 angular_range	— – 0.3050 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	10830000.0000
实空间数据点数 n_real_points	62
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.971; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.958

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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 (4)

Entity 1 polymer

描述 description	IGG1-KAPPA MOPC21 FAB (LIGHT CHAIN)
分子量 formula_weight	23556.0 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	4117

NIVMTQSPKSMSMSVGERVTLTCKASENVVTYVSWYQQKPEQSPKLLIYGASNRYTGVPDRFTGSGSATDFTLTISSVQAEDLADYHCGQGNSYPYTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI 分类编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 2 polymer

描述 description	IGG1-KAPPA MOPC21 FAB (HEAVY CHAIN)
分子量 formula_weight	23856.8 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

DVQLVESGGGLVQPGGSRKLSCAASGFTFSSFGMHWVRQAPEKGLEWVAYISSGSSTLHYADTVKGRFTISRDNPKNTLFLQMTSLRSEDTGMYYCARWGNYPYYAMDYWGQGTSVTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVPRDC

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI 分类编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 3 polymer

描述 description	STREPTOCOCCAL PROTEIN G (DOMAIN III)
分子量 formula_weight	6657.4 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	A

MTPAVTTYKLVINGKTLKGETTTKAVDAETAEKAFKQYANDNGVDGVWTYDDATKTFTVTE

来源 Source

来源生物 organism	Streptococcus sp. G148
NCBI 分类编号 ncbi_taxonomy_id	1324
宿主生物 host_organism	Escherichia coli

Entity 4 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	345

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6. 折叠分类 (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

结构域编号 domain_id	d1igca_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.15 — beta-Grasp (ubiquitin-like)
超家族 Superfamily superfamily	d.15.7 — Immunoglobulin-binding domains
家族 Family family	d.15.7.1 — Immunoglobulin-binding domains

结构域编号 domain_id	d1igch1
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	d1igch2
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	d1igcl1
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	d1igcl2
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 (5 domains)

结构域编号 domain_id	1igcA00
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	1igcH01
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	1igcH02
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	1igcL01
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	1igcL02
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 (7)

;The third IgG-binding domain from streptococcal protein G. An analysis by X-ray crystallography of the structure alone and in a complex with Fab. ;

J.Mol.Biol. (1994)

PMID: 7966308 · DOI: 10.1006/jmbi.1994.1691 PRIMARY

Two Crystal Structures of the B1 Immunoglobulin-Binding Domain of Streptococcal Protein G and Comparison with NMR

Biochemistry (1994)

Crystal Structure of a Streptococcal Protein G Domain Bound to an Fab Fragment

Nature (1992)

;Crystallization and Preliminary Analysis of the Complex between a Mouse Fab Fragment and a Single Igg-Binding Domain from Streptococcal Protein G ;

J.Mol.Biol. (1992)

Determination of the Solution Structures of Domains II and III of Protein G from Streptococcus by 1H Nuclear Magnetic Resonance

J.Mol.Biol. (1992)

;1.67 Angstroms X-Ray Structure of the B2 Immunoglobulin-Binding Domain of Streptococcal Protein G and Comparison to the NMR Structure of the B1 Domain ;

Biochemistry (1992)

A Novel, Highly Stable Fold of the Immunoglobulin Binding Domain of Streptococcal Protein G

Science (1991)

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晶胞边长 a length_a	64.500 Å
晶胞边长 b length_b	70.500 Å
晶胞边长 c length_c	120.100 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	2.600 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.1680
R_work r_work	—
R_free r_free	—

fit	/app/data/saxs_computation/ig/1igc/1igc.fit
pddf	/app/data/pr_computation/ig/1igc/1igc.pr.out
profile	/app/data/saxs_computation/ig/1igc/1igc.dat

IGG1 FAB FRAGMENT (MOPC21) COMPLEX WITH DOMAIN III OF PROTEIN G FROM STREPTOCOCCUS

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

5. 实体与聚合体信息 (4)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 polymer

聚合体 Polymer

来源 Source

Entity 4 water

6. 折叠分类 (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

CATH v4.4 (5 domains)

7. 引用文献 (7)

8. 文件与曲线 (10)

Files (7)

Curves (3)