1dlp

STRUCTURAL CHARACTERIZATION OF THE NATIVE FETUIN-BINDING PROTEIN SCILLA CAMPANULATA AGGLUTININ (SCAFET): A NOVEL TWO-DOMAIN LECTIN

Method: X-RAY DIFFRACTION D_max: 110.9 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	1dlp
沉积日期 deposition_date	1999-12-11
结构标题 title	STRUCTURAL CHARACTERIZATION OF THE NATIVE FETUIN-BINDING PROTEIN SCILLA CAMPANULATA AGGLUTININ (SCAFET): A NOVEL TWO-DOMAIN LECTIN
关键词 keywords	TWO-DOMAIN LECTIN, BETA PRISM II FOLD, NATIVE, 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	39.99 Å
回转半径 Rg (电子) rg_electron	39.08 Å
零角强度 I(0) i0	352988000.00
分子量 molecular_weight	147250.0 kDa
排除体积 excluded_volume	181790 Å³
包络体积 envelope_volume	257170 Å³
水化壳体积 shell_volume	53493 Å³
包络直径 envelope_diameter	108.8 Å
壳层 Rg shell_rg	47.75 Å
包络 Rg envelope_rg	36.58 Å
形状 Rg shape_rg	39.06 Å
总 Rg total_rg	39.63 Å
总原子数 total_atoms	10364
残基数 n_residues	1358
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	110.9 Å
Rg (实空间) rg_real	39.64 Å
Rg 误差 (实空间) rg_real_error	0.57 Å
I(0) (实空间) i0_real	3.5300e+08
I(0) 误差 (实空间) i0_real_error	4.9760e+06
Rg (倒空间) rg_reciprocal	39.86 Å
I(0) (倒空间) i0_reciprocal	353100000.0000
解质量估计 total_estimate	0.8921
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	63.8 Å
偏度 Skewness skewness	-0.128
峰度 Kurtosis kurtosis	-0.912
角度范围 angular_range	— – 0.2000 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	47580000.0000
实空间数据点数 n_real_points	41
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.948; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.749

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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 (2)

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6. 折叠分类 (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

结构域编号 domain_id	d1dlpa1
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	d1dlpa2
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	d1dlpb1
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	d1dlpb2
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	d1dlpc1
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	d1dlpc2
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	d1dlpd1
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	d1dlpd2
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	d1dlpe1
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	d1dlpe2
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	d1dlpf1
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	d1dlpf2
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 (12 domains)

结构域编号 domain_id	1dlpA01
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	1dlpA02
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	1dlpB01
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	1dlpB02
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	1dlpC01
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	1dlpC02
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	1dlpD01
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	1dlpD02
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	1dlpE01
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	1dlpE02
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	1dlpF01
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	1dlpF02
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	277.940 Å
晶胞边长 b length_b	164.100 Å
晶胞边长 c length_c	53.600 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	95.38 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	24

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	3.300 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	—
R_work r_work	0.1890
R_free r_free	0.2930

描述 description	LECTIN SCAFET PRECURSOR
分子量 formula_weight	25545.4 kDa
来源方法 src_method	nat
拷贝数 entity_count	6

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F
原子数 atom_count	10431

STRUCTURAL CHARACTERIZATION OF THE NATIVE FETUIN-BINDING PROTEIN SCILLA CAMPANULATA AGGLUTININ (SCAFET): A NOVEL TWO-DOMAIN LECTIN

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 (2)

Entity 1 polymer

聚合体 Polymer

Entity 2 water

6. 折叠分类 (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. 引用文献 (3)

8. 文件与曲线 (10)

Files (7)

Curves (3)

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	67

fit	/app/data/saxs_computation/dl/1dlp/1dlp.fit
pddf	/app/data/pr_computation/dl/1dlp/1dlp.pr.out
profile	/app/data/saxs_computation/dl/1dlp/1dlp.dat