1k7u

Crystal Structure Analysis of crosslinked-WGA3/GlcNAcbeta1,4GlcNAc complex

Method: X-RAY DIFFRACTION D_max: 74.6 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	1k7u
沉积日期 deposition_date	2001-10-22
结构标题 title	Crystal Structure Analysis of crosslinked-WGA3/GlcNAcbeta1,4GlcNAc complex
关键词 keywords	Hevein-type fold, SUGAR BINDING PROTEIN; SUGAR 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	20.73 Å
回转半径 Rg (电子) rg_electron	20.28 Å
零角强度 I(0) i0	30361600.00
分子量 molecular_weight	35235.0 kDa
排除体积 excluded_volume	40974 Å³
包络体积 envelope_volume	49007 Å³
水化壳体积 shell_volume	20524 Å³
包络直径 envelope_diameter	75.4 Å
壳层 Rg shell_rg	26.60 Å
包络 Rg envelope_rg	20.61 Å
形状 Rg shape_rg	20.34 Å
总 Rg total_rg	20.84 Å
总原子数 total_atoms	2404
残基数 n_residues	340
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	74.6 Å
Rg (实空间) rg_real	20.73 Å
Rg 误差 (实空间) rg_real_error	0.67 Å
I(0) (实空间) i0_real	3.0360e+07
I(0) 误差 (实空间) i0_real_error	4.5330e+05
Rg (倒空间) rg_reciprocal	20.73 Å
I(0) (倒空间) i0_reciprocal	30360000.0000
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	2
主峰位置 r_peak_primary	24.9 Å
偏度 Skewness skewness	0.408
峰度 Kurtosis kurtosis	-0.018
角度范围 angular_range	— – 0.3850 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	2041000.0000
实空间数据点数 n_real_points	70
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.673; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.962; Smooth: 0.990

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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 (3)

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6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d1k7ua1
类 Class class	g — Small proteins
折叠类型 Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
超家族 Superfamily superfamily	g.3.1 — Plant lectins/antimicrobial peptides
家族 Family family	g.3.1.1 — Hevein-like agglutinin (lectin) domain

结构域编号 domain_id	d1k7ua2
类 Class class	g — Small proteins
折叠类型 Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
超家族 Superfamily superfamily	g.3.1 — Plant lectins/antimicrobial peptides
家族 Family family	g.3.1.1 — Hevein-like agglutinin (lectin) domain

结构域编号 domain_id	d1k7ua3
类 Class class	g — Small proteins
折叠类型 Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
超家族 Superfamily superfamily	g.3.1 — Plant lectins/antimicrobial peptides
家族 Family family	g.3.1.1 — Hevein-like agglutinin (lectin) domain

结构域编号 domain_id	d1k7ua4
类 Class class	g — Small proteins
折叠类型 Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
超家族 Superfamily superfamily	g.3.1 — Plant lectins/antimicrobial peptides
家族 Family family	g.3.1.1 — Hevein-like agglutinin (lectin) domain

结构域编号 domain_id	d1k7ub1
类 Class class	g — Small proteins
折叠类型 Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
超家族 Superfamily superfamily	g.3.1 — Plant lectins/antimicrobial peptides
家族 Family family	g.3.1.1 — Hevein-like agglutinin (lectin) domain

结构域编号 domain_id	d1k7ub2
类 Class class	g — Small proteins
折叠类型 Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
超家族 Superfamily superfamily	g.3.1 — Plant lectins/antimicrobial peptides
家族 Family family	g.3.1.1 — Hevein-like agglutinin (lectin) domain

结构域编号 domain_id	d1k7ub3
类 Class class	g — Small proteins
折叠类型 Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
超家族 Superfamily superfamily	g.3.1 — Plant lectins/antimicrobial peptides
家族 Family family	g.3.1.1 — Hevein-like agglutinin (lectin) domain

结构域编号 domain_id	d1k7ub4
类 Class class	g — Small proteins
折叠类型 Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
超家族 Superfamily superfamily	g.3.1 — Plant lectins/antimicrobial peptides
家族 Family family	g.3.1.1 — Hevein-like agglutinin (lectin) domain

CATH v4.4 (8 domains)

结构域编号 domain_id	1k7uA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
同源超家族 H-superfamily homologous superfamily	10 — Endochitinase-like

结构域编号 domain_id	1k7uA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
同源超家族 H-superfamily homologous superfamily	10 — Endochitinase-like

结构域编号 domain_id	1k7uA03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
同源超家族 H-superfamily homologous superfamily	10 — Endochitinase-like

结构域编号 domain_id	1k7uA04
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
同源超家族 H-superfamily homologous superfamily	10 — Endochitinase-like

结构域编号 domain_id	1k7uB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
同源超家族 H-superfamily homologous superfamily	10 — Endochitinase-like

结构域编号 domain_id	1k7uB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
同源超家族 H-superfamily homologous superfamily	10 — Endochitinase-like

结构域编号 domain_id	1k7uB03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
同源超家族 H-superfamily homologous superfamily	10 — Endochitinase-like

结构域编号 domain_id	1k7uB04
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
同源超家族 H-superfamily homologous superfamily	10 — Endochitinase-like

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7. 引用文献 (4)

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晶胞边长 a length_a	44.720 Å
晶胞边长 b length_b	91.550 Å
晶胞边长 c length_c	44.760 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	110.13 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

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	2.200 Å
最低分辨率 resolution_low	8.000 Å
R 因子 r_factor	—
R_work r_work	0.2420
R_free r_free	0.3060

描述 description	agglutinin isolectin 3
分子量 formula_weight	18752.9 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	2493

Crystal Structure Analysis of crosslinked-WGA3/GlcNAcbeta1,4GlcNAc complex

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 (3)

Entity 1 polymer

聚合体 Polymer

Entity 2 branched

Entity 3 water

6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. 引用文献 (4)

8. 文件与曲线 (10)

Files (7)

Curves (3)

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	2

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	89

fit	/app/data/saxs_computation/k7/1k7u/1k7u.fit
pddf	/app/data/pr_computation/k7/1k7u/1k7u.pr.out
profile	/app/data/saxs_computation/k7/1k7u/1k7u.dat