8w4m

Crystal structure of open conformation of human immunoglobulin Fc in presence of EndoSz

Method: X-RAY DIFFRACTION D_max: 80.6 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	8w4m
沉积日期 deposition_date	2023-08-24
结构标题 title	Crystal structure of open conformation of human immunoglobulin Fc in presence of EndoSz
关键词 keywords	N-linked glycan, glycoside hydrolase, transglycosylation, 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	23.19 Å
回转半径 Rg (电子) rg_electron	22.49 Å
零角强度 I(0) i0	12752100.00
分子量 molecular_weight	26044.0 kDa
排除体积 excluded_volume	32135 Å³
包络体积 envelope_volume	40787 Å³
水化壳体积 shell_volume	16241 Å³
包络直径 envelope_diameter	80.5 Å
壳层 Rg shell_rg	27.75 Å
包络 Rg envelope_rg	22.62 Å
形状 Rg shape_rg	22.52 Å
总 Rg total_rg	23.11 Å
总原子数 total_atoms	1796
残基数 n_residues	210
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	80.6 Å
Rg (实空间) rg_real	23.37 Å
Rg 误差 (实空间) rg_real_error	0.83 Å
I(0) (实空间) i0_real	1.2750e+07
I(0) 误差 (实空间) i0_real_error	2.0600e+05
Rg (倒空间) rg_reciprocal	23.33 Å
I(0) (倒空间) i0_reciprocal	12750000.0000
解质量估计 total_estimate	0.8436
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	19.8 Å
偏度 Skewness skewness	0.458
峰度 Kurtosis kurtosis	-0.433
角度范围 angular_range	— – 0.3400 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	2302000.0000
实空间数据点数 n_real_points	66
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.773; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.655; Smooth: 0.989

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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	Immunoglobulin gamma-1 heavy chain
分子量 formula_weight	25129.5 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
原子数 atom_count	1917

TCPPCPAPELLGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSREEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Cricetulus griseus

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)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	1625.5 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 3 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	10

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	121

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7. 引用文献 (1)

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晶胞边长 a length_a	50.088 Å
晶胞边长 b length_b	147.668 Å
晶胞边长 c length_c	75.198 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	C 2 2 21
空间群编号 int_tables_number	20
晶系 crystal_system	—

分辨率 resolution	2.180 Å
最低分辨率 resolution_low	26.340 Å
R 因子 r_factor	0.2103
R_work r_work	0.2080
R_free r_free	0.2550

fit	/app/data/saxs_computation/w4/8w4m/8w4m.fit
pddf	/app/data/pr_computation/w4/8w4m/8w4m.pr.out
profile	/app/data/saxs_computation/w4/8w4m/8w4m.dat

Crystal structure of open conformation of human immunoglobulin Fc in presence of EndoSz

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