SAXSdb — 1ykb

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1ykb
沉积日期 deposition_date	2005-01-17
结构标题 title	Crystal Structure of Insect Cell Expressed IL-22
关键词 keywords	interleukin, cytokine, il-22, glycosylation; CYTOKINE
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	36.93 Å
回转半径 Rg (电子) rg_electron	36.83 Å
零角强度 I(0) i0	162680000.00
分子量 molecular_weight	101880.0 kDa
排除体积 excluded_volume	127350 Å³
包络体积 envelope_volume	164130 Å³
水化壳体积 shell_volume	39332 Å³
包络直径 envelope_diameter	130.3 Å
壳层 Rg shell_rg	40.10 Å
包络 Rg envelope_rg	36.63 Å
形状 Rg shape_rg	36.84 Å
总 Rg total_rg	37.02 Å
总原子数 total_atoms	7128
残基数 n_residues	851
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	122.0 Å
Rg (实空间) rg_real	37.22 Å
Rg 误差 (实空间) rg_real_error	1.10 Å
I(0) (实空间) i0_real	1.6270e+08
I(0) 误差 (实空间) i0_real_error	3.0050e+06
Rg (倒空间) rg_reciprocal	37.04 Å
I(0) (倒空间) i0_reciprocal	162700000.0000
解质量估计 total_estimate	0.8164
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	31.2 Å
偏度 Skewness skewness	0.479
峰度 Kurtosis kurtosis	-0.375
角度范围 angular_range	— – 0.2150 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	84260000.0000
实空间数据点数 n_real_points	44
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.810; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.766; Smooth: 0.414

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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 (6)

Entity 1 polymer

描述 description	PROTEIN (Interleukin-22)
分子量 formula_weight	16402.9 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,C,D,E,F
原子数 atom_count	7197

SHCRLDKSNFQQPYITNRTFMLAKEASLADNNTDVRLIGEKLFHGVSMSERCYLMKQVLNFTLEEVLFPQSDRFQPYMQEVVPFLARLSNRLSTCHIEGDDLHIQRNVQKLKDTVKKLGESGEIKAIGELDLLFMSLRNACI

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

Entity 2 branched

描述 description	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	570.5 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 3 branched

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	424.4 kDa
来源方法 src_method	man
拷贝数 entity_count	4

Entity 4 branched

描述 description	;alpha-D-mannopyranose-(1-6)-alpha-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	894.8 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 5 non-polymer

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	221.2 kDa
来源方法 src_method	man
拷贝数 entity_count	3

Entity 6 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	51

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6. 折叠分类 (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

结构域编号 domain_id	d1ykba_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.26 — 4-helical cytokines
超家族 Superfamily superfamily	a.26.1 — 4-helical cytokines
家族 Family family	a.26.1.3 — Interferons/interleukin-10 (IL-10)

结构域编号 domain_id	d1ykbb_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.26 — 4-helical cytokines
超家族 Superfamily superfamily	a.26.1 — 4-helical cytokines
家族 Family family	a.26.1.3 — Interferons/interleukin-10 (IL-10)

结构域编号 domain_id	d1ykbc_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.26 — 4-helical cytokines
超家族 Superfamily superfamily	a.26.1 — 4-helical cytokines
家族 Family family	a.26.1.3 — Interferons/interleukin-10 (IL-10)

结构域编号 domain_id	d1ykbd_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.26 — 4-helical cytokines
超家族 Superfamily superfamily	a.26.1 — 4-helical cytokines
家族 Family family	a.26.1.3 — Interferons/interleukin-10 (IL-10)

结构域编号 domain_id	d1ykbe_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.26 — 4-helical cytokines
超家族 Superfamily superfamily	a.26.1 — 4-helical cytokines
家族 Family family	a.26.1.3 — Interferons/interleukin-10 (IL-10)

结构域编号 domain_id	d1ykbf_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.26 — 4-helical cytokines
超家族 Superfamily superfamily	a.26.1 — 4-helical cytokines
家族 Family family	a.26.1.3 — Interferons/interleukin-10 (IL-10)

CATH v4.4 (6 domains)

结构域编号 domain_id	1ykbA00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1250 — Growth Hormone; Chain: A;
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1ykbB00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1250 — Growth Hormone; Chain: A;
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1ykbC00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1250 — Growth Hormone; Chain: A;
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1ykbD00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1250 — Growth Hormone; Chain: A;
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1ykbE00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1250 — Growth Hormone; Chain: A;
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1ykbF00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1250 — Growth Hormone; Chain: A;
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	64.877 Å
晶胞边长 b length_b	62.227 Å
晶胞边长 c length_c	139.524 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	91.35 °
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	—

分辨率 resolution	2.600 Å
最低分辨率 resolution_low	19.930 Å
R 因子 r_factor	—
R_work r_work	0.2320
R_free r_free	0.2650

fit	/app/data/saxs_computation/yk/1ykb/1ykb.fit
pddf	/app/data/pr_computation/yk/1ykb/1ykb.pr.out
profile	/app/data/saxs_computation/yk/1ykb/1ykb.dat

Crystal Structure of Insect Cell Expressed IL-22

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 (6)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 branched

Entity 3 branched

Entity 4 branched

Entity 5 non-polymer

Entity 6 water

6. 折叠分类 (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)