2dp8

;Carbohydrate recognition by lactoferrin: Crystal structure of the complex of C-terminal lobe of bovine lactoferrin with trisaccharide at 2.5 A resolution ;

Method: X-RAY DIFFRACTION D_max: 66.0 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	2dp8
沉积日期 deposition_date	2006-05-08
结构标题 title	;Carbohydrate recognition by lactoferrin: Crystal structure of the complex of C-terminal lobe of bovine lactoferrin with trisaccharide at 2.5 A resolution ;
关键词 keywords	C lobe, complex, Saccharide, METAL BINDING PROTEIN; METAL 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	21.11 Å
回转半径 Rg (电子) rg_electron	19.99 Å
零角强度 I(0) i0	30649900.00
分子量 molecular_weight	40516.0 kDa
排除体积 excluded_volume	49867 Å³
包络体积 envelope_volume	60021 Å³
水化壳体积 shell_volume	24270 Å³
包络直径 envelope_diameter	67.6 Å
壳层 Rg shell_rg	27.28 Å
包络 Rg envelope_rg	20.26 Å
形状 Rg shape_rg	19.95 Å
总 Rg total_rg	21.01 Å
总原子数 total_atoms	2819
残基数 n_residues	341
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	66.0 Å
Rg (实空间) rg_real	20.97 Å
Rg 误差 (实空间) rg_real_error	0.28 Å
I(0) (实空间) i0_real	3.0650e+07
I(0) 误差 (实空间) i0_real_error	3.6900e+05
Rg (倒空间) rg_reciprocal	20.99 Å
I(0) (倒空间) i0_reciprocal	30650000.0000
解质量估计 total_estimate	0.8962
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	26.2 Å
偏度 Skewness skewness	0.146
峰度 Kurtosis kurtosis	-0.428
角度范围 angular_range	— – 0.3750 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	6997000.0000
实空间数据点数 n_real_points	69
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.890; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.990

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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 (10)

Entity 1 polymer

描述 description	Lactotransferrin
分子量 formula_weight	37655.5 kDa
EC 编号 ec_number	3.4.21.-
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	2984

YTRVVWCAVGPEEQKKCQQWSQQSGQNVTCATASTTDDCIVLVLKGEADALNLDGGYIYTAGKCGLVPVLAENRKSSKHSSLDCVLRPTEGYLAVAVVKKANEGLTWNSLKDKKSCHTAVDRTAGWNIPMGLIVNQTGSCAFDEFFSQSCAPGADPKSRLCALCAGDDQGLDKCVPNSKEKYYGYTGAFRCLAEDVGDVAFVKNDTVWENTNGESTADWAKNLKREDFRLLCLDGTRKPVTEAQSCHLAVAPNHAVVSRSDRAAHVEQVLLHQQALFGKNGKNCPDKFCLFKSETKNLLFNDNTECLAKLGGRPTYEEYLGTEYVTAIANLKKCSTSPLLEACAF

Entity 2 branched

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	424.4 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 3 branched

描述 description	;alpha-D-mannopyranose-(1-4)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	910.8 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 4 branched

描述 description	;alpha-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	1073.0 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 5 branched

描述 description	;2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	627.6 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 6 non-polymer

描述 description	FE (III) ION
分子量 formula_weight	55.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 7 non-polymer

描述 description	CARBONATE ION
分子量 formula_weight	60.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 8 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 9 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 10 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	165

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6. 折叠分类 (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

结构域编号 domain_id	d2dp8a_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.94 — Periplasmic binding protein-like II
超家族 Superfamily superfamily	c.94.1 — Periplasmic binding protein-like II
家族 Family family	c.94.1.0 — automated matches

CATH v4.4 (2 domains)

结构域编号 domain_id	2dp8A01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Periplasmic binding protein-like II

结构域编号 domain_id	2dp8A02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Periplasmic binding protein-like II

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7. 引用文献 (1)

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晶胞边长 a length_a	63.082 Å
晶胞边长 b length_b	50.437 Å
晶胞边长 c length_c	65.790 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	107.53 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	2

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	2.500 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.1847
R_work r_work	0.1839
R_free r_free	0.2003

fit	/app/data/saxs_computation/dp/2dp8/2dp8.fit
pddf	/app/data/pr_computation/dp/2dp8/2dp8.pr.out
profile	/app/data/saxs_computation/dp/2dp8/2dp8.dat