1y2x

;Crystal structure of the tetragonal form of the common edible mushroom (Agaricus bisporus) lectin in complex with T-antigen and N-acetylglucosamine ;

Method: X-RAY DIFFRACTION D_max: 74.1 Å Quality: EXCELLENT

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	1y2x
沉积日期 deposition_date	2004-11-23
结构标题 title	;Crystal structure of the tetragonal form of the common edible mushroom (Agaricus bisporus) lectin in complex with T-antigen and N-acetylglucosamine ;
关键词 keywords	ABL, Agaricus bisporus, lectin, mushroom, T-antigen, 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	25.11 Å
回转半径 Rg (电子) rg_electron	23.95 Å
零角强度 I(0) i0	76949800.00
分子量 molecular_weight	66990.0 kDa
排除体积 excluded_volume	83036 Å³
包络体积 envelope_volume	95428 Å³
水化壳体积 shell_volume	32213 Å³
包络直径 envelope_diameter	75.9 Å
壳层 Rg shell_rg	32.10 Å
包络 Rg envelope_rg	23.87 Å
形状 Rg shape_rg	23.92 Å
总 Rg total_rg	24.87 Å
总原子数 total_atoms	4728
残基数 n_residues	568
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	74.1 Å
Rg (实空间) rg_real	24.96 Å
Rg 误差 (实空间) rg_real_error	0.36 Å
I(0) (实空间) i0_real	7.6950e+07
I(0) 误差 (实空间) i0_real_error	8.6640e+05
Rg (倒空间) rg_reciprocal	25.01 Å
I(0) (倒空间) i0_reciprocal	76950000.0000
解质量估计 total_estimate	0.9106
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	31.7 Å
偏度 Skewness skewness	0.093
峰度 Kurtosis kurtosis	-0.571
角度范围 angular_range	— – 0.3150 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	14850000.0000
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: 0.970; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.935

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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	lectin
分子量 formula_weight	16069.8 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	4790

TYTISIRVYQTTPKGFFRPVERTNWKYANGGTWDEVRGEYVLTMGGSGTSGSLRFVSSDTDESFVATFGVHNYKRWCDIVTNLTNEQTALVINQEYYGVPIRDQARENQLTSYNVANAKGRRFAIEYTVTEGDNLKANLIIG

Entity 2 branched

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

Entity 3 non-polymer

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	221.2 kDa
来源方法 src_method	man
拷贝数 entity_count	4

Entity 4 non-polymer

描述 description	SERINE
分子量 formula_weight	105.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

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	62

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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	d1y2xa_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.97 — Cytolysin/lectin
超家族 Superfamily superfamily	b.97.1 — Cytolysin/lectin
家族 Family family	b.97.1.2 — Fungal fruit body lectin

结构域编号 domain_id	d1y2xb_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.97 — Cytolysin/lectin
超家族 Superfamily superfamily	b.97.1 — Cytolysin/lectin
家族 Family family	b.97.1.2 — Fungal fruit body lectin

结构域编号 domain_id	d1y2xc_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.97 — Cytolysin/lectin
超家族 Superfamily superfamily	b.97.1 — Cytolysin/lectin
家族 Family family	b.97.1.2 — Fungal fruit body lectin

结构域编号 domain_id	d1y2xd_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.97 — Cytolysin/lectin
超家族 Superfamily superfamily	b.97.1 — Cytolysin/lectin
家族 Family family	b.97.1.2 — Fungal fruit body lectin

CATH v4.4 (4 domains)

结构域编号 domain_id	1y2xA00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	270 — Mutm (Fpg) Protein; Chain: A, domain 2
同源超家族 H-superfamily homologous superfamily	20 — Cytolysin/lectin

结构域编号 domain_id	1y2xB00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	270 — Mutm (Fpg) Protein; Chain: A, domain 2
同源超家族 H-superfamily homologous superfamily	20 — Cytolysin/lectin

结构域编号 domain_id	1y2xC00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	270 — Mutm (Fpg) Protein; Chain: A, domain 2
同源超家族 H-superfamily homologous superfamily	20 — Cytolysin/lectin

结构域编号 domain_id	1y2xD00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	270 — Mutm (Fpg) Protein; Chain: A, domain 2
同源超家族 H-superfamily homologous superfamily	20 — Cytolysin/lectin

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7. 引用文献 (2)

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晶胞边长 a length_a	85.675 Å
晶胞边长 b length_b	85.675 Å
晶胞边长 c length_c	257.073 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	32

空间群 space_group	P 43 21 2
空间群编号 int_tables_number	96
晶系 crystal_system	—

分辨率 resolution	2.360 Å
最低分辨率 resolution_low	30.000 Å
R 因子 r_factor	0.2288
R_work r_work	0.2276
R_free r_free	0.2524

fit	/app/data/saxs_computation/y2/1y2x/1y2x.fit
pddf	/app/data/pr_computation/y2/1y2x/1y2x.pr.out
profile	/app/data/saxs_computation/y2/1y2x/1y2x.dat