SAXSdb — 1h3v

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1h3v
沉积日期 deposition_date	2002-09-19
结构标题 title	CRYSTAL STRUCTURE OF THE HUMAN IGG1 FC-FRAGMENT,GLYCOFORM (G2F)2,SG P212121
关键词 keywords	IMMUNOGLOBULIN/FC-FRAGMENT, FC-FRAGMENT, GLYCOSYLATION, FCGR, ANTIBODY, EFFECTOR FUNCTIONS, 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	26.77 Å
回转半径 Rg (电子) rg_electron	25.49 Å
零角强度 I(0) i0	41055800.00
分子量 molecular_weight	49875.0 kDa
排除体积 excluded_volume	62509 Å³
包络体积 envelope_volume	80356 Å³
水化壳体积 shell_volume	26116 Å³
包络直径 envelope_diameter	81.1 Å
壳层 Rg shell_rg	33.07 Å
包络 Rg envelope_rg	24.99 Å
形状 Rg shape_rg	25.49 Å
总 Rg total_rg	26.36 Å
总原子数 total_atoms	3509
残基数 n_residues	415
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	77.6 Å
Rg (实空间) rg_real	26.61 Å
Rg 误差 (实空间) rg_real_error	0.43 Å
I(0) (实空间) i0_real	4.1060e+07
I(0) 误差 (实空间) i0_real_error	5.6320e+05
Rg (倒空间) rg_reciprocal	26.67 Å
I(0) (倒空间) i0_reciprocal	41060000.0000
解质量估计 total_estimate	0.9183
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	38.1 Å
偏度 Skewness skewness	0.023
峰度 Kurtosis kurtosis	-0.695
角度范围 angular_range	— – 0.2950 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	4889000.0000
实空间数据点数 n_real_points	60
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.990; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.965

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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	IG GAMMA-1 CHAIN C REGION
分子量 formula_weight	25126.5 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	3600

TCPPCPAPELLGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPQVKFNWYVDGVQVHNAKTKPREQQYNSTYRVVSVLTVLHQNWLDGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSREEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK

Entity 2 branched

描述 description	;beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	1422.3 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 3 branched

描述 description	;beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-beta-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	1422.3 kDa
来源方法 src_method	man
拷贝数 entity_count	1

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	91

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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	d1h3va1
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	d1h3va2
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	d1h3vb1
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	d1h3vb2
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	1h3vA01
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	1h3vA02
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	1h3vB01
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	1h3vB02
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	49.470 Å
晶胞边长 b length_b	80.850 Å
晶胞边长 c length_c	141.750 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	8

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	3.100 Å
最低分辨率 resolution_low	50.000 Å
R 因子 r_factor	0.2400
R_work r_work	0.2400
R_free r_free	0.3140

fit	/app/data/saxs_computation/h3/1h3v/1h3v.fit
pddf	/app/data/pr_computation/h3/1h3v/1h3v.pr.out
profile	/app/data/saxs_computation/h3/1h3v/1h3v.dat

CRYSTAL STRUCTURE OF THE HUMAN IGG1 FC-FRAGMENT,GLYCOFORM (G2F)2,SG P212121

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