SAXSdb — 1xxq

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1xxq
沉积日期 deposition_date	2004-11-08
结构标题 title	Structure of a mannose-specific jacalin-related lectin from Morus nigra
关键词 keywords	tetrameric b-prism fold, jacalin-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	27.26 Å
回转半径 Rg (电子) rg_electron	26.35 Å
零角强度 I(0) i0	68468500.00
分子量 molecular_weight	66070.0 kDa
排除体积 excluded_volume	83161 Å³
包络体积 envelope_volume	96613 Å³
水化壳体积 shell_volume	30878 Å³
包络直径 envelope_diameter	86.9 Å
壳层 Rg shell_rg	33.34 Å
包络 Rg envelope_rg	26.37 Å
形状 Rg shape_rg	26.33 Å
总 Rg total_rg	27.16 Å
总原子数 total_atoms	4681
残基数 n_residues	616
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	85.2 Å
Rg (实空间) rg_real	27.22 Å
Rg 误差 (实空间) rg_real_error	0.55 Å
I(0) (实空间) i0_real	6.8470e+07
I(0) 误差 (实空间) i0_real_error	9.4130e+05
Rg (倒空间) rg_reciprocal	27.23 Å
I(0) (倒空间) i0_reciprocal	68470000.0000
解质量估计 total_estimate	0.8984
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	33.8 Å
偏度 Skewness skewness	0.304
峰度 Kurtosis kurtosis	-0.382
角度范围 angular_range	— – 0.2900 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	14910000.0000
实空间数据点数 n_real_points	59
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.933; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.877

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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 (5)

Entity 1 polymer

描述 description	mannose-binding lectin
分子量 formula_weight	17036.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	5256

MAGTSTNTQTTGTSQTIEVGLWGGPGGNAWDDGSYTGIREINLSHGDAIGAFSVIYDLNGQPFTGPTHPGNEPSFKTVKITLDFPNEFLVSVSGYTGVLARLATGKDVIRSLTFKTNKKTYGPYGKEEGTPFSLPIENGLIVGFKGRSGFVVDAIGFHLSL

Entity 2 non-polymer

描述 description	ACETIC ACID
分子量 formula_weight	60.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 3 non-polymer

描述 description	GLYCEROL
分子量 formula_weight	92.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 4 non-polymer

描述 description	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 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	575

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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	d1xxqa_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.77 — beta-Prism I
超家族 Superfamily superfamily	b.77.3 — Mannose-binding lectins
家族 Family family	b.77.3.1 — Mannose-binding lectins

结构域编号 domain_id	d1xxqb_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.77 — beta-Prism I
超家族 Superfamily superfamily	b.77.3 — Mannose-binding lectins
家族 Family family	b.77.3.1 — Mannose-binding lectins

结构域编号 domain_id	d1xxqc_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.77 — beta-Prism I
超家族 Superfamily superfamily	b.77.3 — Mannose-binding lectins
家族 Family family	b.77.3.1 — Mannose-binding lectins

结构域编号 domain_id	d1xxqd_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.77 — beta-Prism I
超家族 Superfamily superfamily	b.77.3 — Mannose-binding lectins
家族 Family family	b.77.3.1 — Mannose-binding lectins

CATH v4.4 (4 domains)

结构域编号 domain_id	1xxqA00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	100 — Aligned Prism
拓扑 Topology topology	10 — Vitelline Membrane Outer Layer Protein I, subunit A
同源超家族 H-superfamily homologous superfamily	30 — Jacalin-like lectin domain

结构域编号 domain_id	1xxqB00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	100 — Aligned Prism
拓扑 Topology topology	10 — Vitelline Membrane Outer Layer Protein I, subunit A
同源超家族 H-superfamily homologous superfamily	30 — Jacalin-like lectin domain

结构域编号 domain_id	1xxqC00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	100 — Aligned Prism
拓扑 Topology topology	10 — Vitelline Membrane Outer Layer Protein I, subunit A
同源超家族 H-superfamily homologous superfamily	30 — Jacalin-like lectin domain

结构域编号 domain_id	1xxqD00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	100 — Aligned Prism
拓扑 Topology topology	10 — Vitelline Membrane Outer Layer Protein I, subunit A
同源超家族 H-superfamily homologous superfamily	30 — Jacalin-like lectin domain

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7. 引用文献 (1)

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晶胞边长 a length_a	110.740 Å
晶胞边长 b length_b	110.740 Å
晶胞边长 c length_c	159.280 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	120.00 °
晶胞分子数 Z z_pdb	24

空间群 space_group	P 65
空间群编号 int_tables_number	170
晶系 crystal_system	—

分辨率 resolution	1.800 Å
最低分辨率 resolution_low	21.850 Å
R 因子 r_factor	0.1900
R_work r_work	0.1900
R_free r_free	0.2100

fit	/app/data/saxs_computation/xx/1xxq/1xxq.fit
pddf	/app/data/pr_computation/xx/1xxq/1xxq.pr.out
profile	/app/data/saxs_computation/xx/1xxq/1xxq.dat

Structure of a mannose-specific jacalin-related lectin from Morus nigra

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 (5)

Entity 1 polymer

聚合体 Polymer

Entity 2 non-polymer

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 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 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)