SAXSdb — 2arx

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2arx
沉积日期 deposition_date	2005-08-22
结构标题 title	Pterocarpus angolensis seed lectin in complex with the decasaccharide NA2F
关键词 keywords	lectin, carbohydrate, legume lectin, 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	27.10 Å
回转半径 Rg (电子) rg_electron	26.03 Å
零角强度 I(0) i0	50262600.00
分子量 molecular_weight	54413.0 kDa
排除体积 excluded_volume	67556 Å³
包络体积 envelope_volume	78715 Å³
水化壳体积 shell_volume	26109 Å³
包络直径 envelope_diameter	91.0 Å
壳层 Rg shell_rg	32.36 Å
包络 Rg envelope_rg	26.08 Å
形状 Rg shape_rg	26.03 Å
总 Rg total_rg	26.70 Å
总原子数 total_atoms	3826
残基数 n_residues	480
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	87.9 Å
Rg (实空间) rg_real	27.23 Å
Rg 误差 (实空间) rg_real_error	0.64 Å
I(0) (实空间) i0_real	5.0260e+07
I(0) 误差 (实空间) i0_real_error	7.5220e+05
Rg (倒空间) rg_reciprocal	27.19 Å
I(0) (倒空间) i0_reciprocal	50260000.0000
解质量估计 total_estimate	0.8764
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	26.8 Å
偏度 Skewness skewness	0.424
峰度 Kurtosis kurtosis	-0.487
角度范围 angular_range	— – 0.2950 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	7645000.0000
实空间数据点数 n_real_points	60
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.864; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.890; Smooth: 0.906

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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 (7)

Entity 1 polymer

描述 description	lectin
分子量 formula_weight	27575.3 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	4038

QDSLSFGFPTFPSDQKNLIFQGDAQIKNNAVQLTKTDSNGNPVASTVGRILFSAQVHLWEKSSSRVANFQSQFSFSLKSPLSNGADGIAFFIAPPDTTIPSGSGGGLLGLFAPGTAQNTSANQVIAVEFDTFYAQDSNTWDPNYPHIGIDVNSIRSVKTVKWDRRDGQSLNVLVTFNPSTRNLDVVATYSDGTRYEVSYEVDVRSVLPEWVRVGFSAASGEQYQTHTLESWSFTSTLLYTAQKKGENLALEM

Entity 2 branched

描述 description	alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose
分子量 formula_weight	342.3 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 3 branched

描述 description	;beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose ;
分子量 formula_weight	1276.2 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 4 non-polymer

描述 description	MANGANESE (II) ION
分子量 formula_weight	54.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 5 non-polymer

描述 description	CALCIUM ION
分子量 formula_weight	40.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 6 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	1

Entity 7 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	210

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6. 折叠分类 (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d2arxa_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.29 — Concanavalin A-like lectins/glucanases
超家族 Superfamily superfamily	b.29.1 — Concanavalin A-like lectins/glucanases
家族 Family family	b.29.1.1 — Legume lectins

结构域编号 domain_id	d2arxb_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.29 — Concanavalin A-like lectins/glucanases
超家族 Superfamily superfamily	b.29.1 — Concanavalin A-like lectins/glucanases
家族 Family family	b.29.1.1 — Legume lectins

CATH v4.4 (2 domains)

结构域编号 domain_id	2arxA00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	200 —

结构域编号 domain_id	2arxB00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	200 —

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7. 引用文献 (1)

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晶胞边长 a length_a	56.780 Å
晶胞边长 b length_b	83.320 Å
晶胞边长 c length_c	122.380 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	8

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	2.000 Å
最低分辨率 resolution_low	15.000 Å
R 因子 r_factor	0.1790
R_work r_work	0.1760
R_free r_free	0.2160

fit	/app/data/saxs_computation/ar/2arx/2arx.fit
pddf	/app/data/pr_computation/ar/2arx/2arx.pr.out
profile	/app/data/saxs_computation/ar/2arx/2arx.dat

Pterocarpus angolensis seed lectin in complex with the decasaccharide NA2F

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution