SAXSdb — 1kj1

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1kj1
沉积日期 deposition_date	2001-12-04
结构标题 title	MANNOSE-SPECIFIC AGGLUTININ (LECTIN) FROM GARLIC (ALLIUM SATIVUM) BULBS COMPLEXED WITH ALPHA-D-MANNOSE
关键词 keywords	BULB LECTIN, MANNOSE, PLANT PROTEIN; PLANT 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	27.10 Å
回转半径 Rg (电子) rg_electron	26.29 Å
零角强度 I(0) i0	45634700.00
分子量 molecular_weight	50774.0 kDa
排除体积 excluded_volume	62688 Å³
包络体积 envelope_volume	77031 Å³
水化壳体积 shell_volume	25139 Å³
包络直径 envelope_diameter	89.1 Å
壳层 Rg shell_rg	32.57 Å
包络 Rg envelope_rg	25.97 Å
形状 Rg shape_rg	26.25 Å
总 Rg total_rg	27.05 Å
总原子数 total_atoms	3570
残基数 n_residues	436
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	87.4 Å
Rg (实空间) rg_real	27.08 Å
Rg 误差 (实空间) rg_real_error	0.54 Å
I(0) (实空间) i0_real	4.5630e+07
I(0) 误差 (实空间) i0_real_error	6.6650e+05
Rg (倒空间) rg_reciprocal	27.09 Å
I(0) (倒空间) i0_reciprocal	45630000.0000
解质量估计 total_estimate	0.9040
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	28.2 Å
偏度 Skewness skewness	0.255
峰度 Kurtosis kurtosis	-0.539
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	6088000.0000
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: 0.937; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.954; Smooth: 0.981

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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	lectin I
分子量 formula_weight	11988.2 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,P
原子数 atom_count	3745

RNLLTNGEGLYAGQSLDVEPYHFIMQEDCNLVLYDHSTSVWASNTGILGKKGCKAVLQSDGNFVVYDAEGRSLWASHSVRGNGNYVLVLQEDGNVVIYGSDIWSTGTYK

Entity 2 polymer

描述 description	lectin II
分子量 formula_weight	12169.4 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	D,Q

RNILMNDEGLYAGQSLDVEPYHLIMQEDCNLVLYDHSTAVWTTNTDIPGKKGCKAVLQSDGNFVVYDAEGRSLWASHSVRGNGNYVLVLQEDGNVVIYGSDIWSTNTYK

Entity 3 non-polymer

描述 description	alpha-D-mannopyranose
分子量 formula_weight	180.2 kDa
来源方法 src_method	man
拷贝数 entity_count	14

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	175

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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	d1kj1a_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.78 — beta-Prism II
超家族 Superfamily superfamily	b.78.1 — alpha-D-mannose-specific plant lectins
家族 Family family	b.78.1.1 — alpha-D-mannose-specific plant lectins

结构域编号 domain_id	d1kj1d_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.78 — beta-Prism II
超家族 Superfamily superfamily	b.78.1 — alpha-D-mannose-specific plant lectins
家族 Family family	b.78.1.1 — alpha-D-mannose-specific plant lectins

结构域编号 domain_id	d1kj1p_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.78 — beta-Prism II
超家族 Superfamily superfamily	b.78.1 — alpha-D-mannose-specific plant lectins
家族 Family family	b.78.1.1 — alpha-D-mannose-specific plant lectins

结构域编号 domain_id	d1kj1q_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.78 — beta-Prism II
超家族 Superfamily superfamily	b.78.1 — alpha-D-mannose-specific plant lectins
家族 Family family	b.78.1.1 — alpha-D-mannose-specific plant lectins

CATH v4.4 (4 domains)

结构域编号 domain_id	1kj1A00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	90 — Orthogonal Prism
拓扑 Topology topology	10 — Agglutinin, subunit A
同源超家族 H-superfamily homologous superfamily	10 — Bulb-type lectin domain

结构域编号 domain_id	1kj1D00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	90 — Orthogonal Prism
拓扑 Topology topology	10 — Agglutinin, subunit A
同源超家族 H-superfamily homologous superfamily	10 — Bulb-type lectin domain

结构域编号 domain_id	1kj1P00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	90 — Orthogonal Prism
拓扑 Topology topology	10 — Agglutinin, subunit A
同源超家族 H-superfamily homologous superfamily	10 — Bulb-type lectin domain

结构域编号 domain_id	1kj1Q00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	90 — Orthogonal Prism
拓扑 Topology topology	10 — Agglutinin, subunit A
同源超家族 H-superfamily homologous superfamily	10 — Bulb-type lectin domain

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7. 引用文献 (3)

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晶胞边长 a length_a	201.831 Å
晶胞边长 b length_b	43.516 Å
晶胞边长 c length_c	78.736 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	112.26 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	—

分辨率 resolution	2.200 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.2110
R_work r_work	0.2110
R_free r_free	0.2510

fit	/app/data/saxs_computation/kj/1kj1/1kj1.fit
pddf	/app/data/pr_computation/kj/1kj1/1kj1.pr.out
profile	/app/data/saxs_computation/kj/1kj1/1kj1.dat

MANNOSE-SPECIFIC AGGLUTININ (LECTIN) FROM GARLIC (ALLIUM SATIVUM) BULBS COMPLEXED WITH ALPHA-D-MANNOSE

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 (4)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

Entity 3 non-polymer

Entity 4 water

6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. 引用文献 (3)

8. 文件与曲线 (10)

Files (7)

Curves (3)