SAXSdb — 1m26

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1m26
沉积日期 deposition_date	2002-06-21
结构标题 title	Crystal structure of jacalin-T-antigen complex
关键词 keywords	All beta sheet protein, beta prism I fold, SUGAR BINDING PROTEIN, PLANT PROTEIN; SUGAR BINDING 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	27.81 Å
回转半径 Rg (电子) rg_electron	26.85 Å
零角强度 I(0) i0	64575800.00
分子量 molecular_weight	66176.0 kDa
排除体积 excluded_volume	84013 Å³
包络体积 envelope_volume	99465 Å³
水化壳体积 shell_volume	31195 Å³
包络直径 envelope_diameter	92.6 Å
壳层 Rg shell_rg	34.01 Å
包络 Rg envelope_rg	26.77 Å
形状 Rg shape_rg	26.85 Å
总 Rg total_rg	27.61 Å
总原子数 total_atoms	4688
残基数 n_residues	594
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	91.4 Å
Rg (实空间) rg_real	27.76 Å
Rg 误差 (实空间) rg_real_error	0.59 Å
I(0) (实空间) i0_real	6.4580e+07
I(0) 误差 (实空间) i0_real_error	9.8590e+05
Rg (倒空间) rg_reciprocal	27.78 Å
I(0) (倒空间) i0_reciprocal	64580000.0000
解质量估计 total_estimate	0.8974
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	35.3 Å
偏度 Skewness skewness	0.272
峰度 Kurtosis kurtosis	-0.447
角度范围 angular_range	— – 0.2850 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	15360000.0000
实空间数据点数 n_real_points	58
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.892; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.991

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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	Jacalin, alpha chain
分子量 formula_weight	14673.5 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,C,E,G
原子数 atom_count	5187

GKAFDDGAFTGIREINLSYNKETAIGDFQVVYDLNGSPYVGQNHKSFITGFTPVKISLDFPSEYIMEVSGYTGNVSGYVVVRSLTFKTNKKTYGPYGVTSGTPFNLPIENGLIVGFKGSIGYWLDYFSMYLSL

Entity 2 polymer

描述 description	Jacalin, beta chain
分子量 formula_weight	1658.9 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	B,D,F,H

SGISQTVIVGPWGAKSA

Entity 3 branched

描述 description	beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose
分子量 formula_weight	383.3 kDa
来源方法 src_method	man
拷贝数 entity_count	4

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	497

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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	d1m26.1
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	d1m26.2
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	d1m26.3
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	d1m26.4
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	1m26A00
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	1m26C00
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	1m26E00
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	1m26G00
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 (2)

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晶胞边长 a length_a	58.920 Å
晶胞边长 b length_b	78.000 Å
晶胞边长 c length_c	67.910 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	100.73 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

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	1.620 Å
最低分辨率 resolution_low	19.580 Å
R 因子 r_factor	0.1890
R_work r_work	0.1890
R_free r_free	0.2060

fit	/app/data/saxs_computation/m2/1m26/1m26.fit
pddf	/app/data/pr_computation/m2/1m26/1m26.pr.out
profile	/app/data/saxs_computation/m2/1m26/1m26.dat

Crystal structure of jacalin-T-antigen 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

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 branched

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 (2)

8. 文件与曲线 (10)

Files (7)

Curves (3)