1msa

MANNOSE-SPECIFIC AGGLUTININ (LECTIN) FROM SNOWDROP (GALANTHUS NIVALIS) BULBS COMPLEXED WITH METHYL-ALPHA-D-MANNOSIDE

Method: X-RAY DIFFRACTION D_max: 70.3 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	1msa
沉积日期 deposition_date	1995-03-06
结构标题 title	MANNOSE-SPECIFIC AGGLUTININ (LECTIN) FROM SNOWDROP (GALANTHUS NIVALIS) BULBS COMPLEXED WITH METHYL-ALPHA-D-MANNOSIDE
关键词 keywords	METHYL-ALPHA-D-MANNOSIDE, LECTIN (AGGLUTININ); LECTIN (AGGLUTININ)
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	24.94 Å
回转半径 Rg (电子) rg_electron	23.63 Å
零角强度 I(0) i0	44214800.00
分子量 molecular_weight	50532.0 kDa
排除体积 excluded_volume	62534 Å³
包络体积 envelope_volume	72532 Å³
水化壳体积 shell_volume	25296 Å³
包络直径 envelope_diameter	69.0 Å
壳层 Rg shell_rg	31.03 Å
包络 Rg envelope_rg	23.41 Å
形状 Rg shape_rg	23.59 Å
总 Rg total_rg	24.54 Å
总原子数 total_atoms	3548
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	70.3 Å
Rg (实空间) rg_real	24.74 Å
Rg 误差 (实空间) rg_real_error	0.38 Å
I(0) (实空间) i0_real	4.4210e+07
I(0) 误差 (实空间) i0_real_error	5.5140e+05
Rg (倒空间) rg_reciprocal	24.79 Å
I(0) (倒空间) i0_reciprocal	44220000.0000
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	34.6 Å
偏度 Skewness skewness	-0.023
峰度 Kurtosis kurtosis	-0.782
角度范围 angular_range	— – 0.3200 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	5257000.0000
实空间数据点数 n_real_points	64
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.990; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.000

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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) 8 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1msaa_
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	d1msab_
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	d1msac_
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	d1msad_
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	1msaA00
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	1msaB00
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	1msaC00
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	1msaD00
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	138.820 Å
晶胞边长 b length_b	64.110 Å
晶胞边长 c length_c	62.080 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	16

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	2.290 Å
最低分辨率 resolution_low	8.000 Å
R 因子 r_factor	0.1770
R_work r_work	0.1770
R_free r_free	0.2400

描述 description	AGGLUTININ
分子量 formula_weight	12061.3 kDa
来源方法 src_method	nat
拷贝数 entity_count	4

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	3875

MANNOSE-SPECIFIC AGGLUTININ (LECTIN) FROM SNOWDROP (GALANTHUS NIVALIS) BULBS COMPLEXED WITH METHYL-ALPHA-D-MANNOSIDE

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 non-polymer

Entity 3 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)

描述 description	methyl alpha-D-mannopyranoside
分子量 formula_weight	194.2 kDa
来源方法 src_method	man
拷贝数 entity_count	12

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	327

fit	/app/data/saxs_computation/ms/1msa/1msa.fit
pddf	/app/data/pr_computation/ms/1msa/1msa.pr.out
profile	/app/data/saxs_computation/ms/1msa/1msa.dat