SAXSdb — 2ggu

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2ggu
沉积日期 deposition_date	2006-03-24
结构标题 title	;crystal structure of the trimeric neck and carbohydrate recognition domain of human surfactant protein D in complex with maltotriose ;
关键词 keywords	protein-carbohydrate ligand complex, 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	26.87 Å
回转半径 Rg (电子) rg_electron	25.58 Å
零角强度 I(0) i0	45771500.00
分子量 molecular_weight	51060.0 kDa
排除体积 excluded_volume	63313 Å³
包络体积 envelope_volume	75959 Å³
水化壳体积 shell_volume	25834 Å³
包络直径 envelope_diameter	81.4 Å
壳层 Rg shell_rg	31.62 Å
包络 Rg envelope_rg	25.67 Å
形状 Rg shape_rg	25.52 Å
总 Rg total_rg	26.44 Å
总原子数 total_atoms	3573
残基数 n_residues	453
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	77.9 Å
Rg (实空间) rg_real	26.73 Å
Rg 误差 (实空间) rg_real_error	0.53 Å
I(0) (实空间) i0_real	4.5770e+07
I(0) 误差 (实空间) i0_real_error	6.3950e+05
Rg (倒空间) rg_reciprocal	26.78 Å
I(0) (倒空间) i0_reciprocal	45770000.0000
解质量估计 total_estimate	0.9133
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	39.6 Å
偏度 Skewness skewness	0.011
峰度 Kurtosis kurtosis	-0.787
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	17120000.0000
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: 0.971; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.960

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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	Pulmonary surfactant-associated protein D
分子量 formula_weight	17272.2 kDa
来源方法 src_method	man
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C
原子数 atom_count	3848

AMADIGSDVASLRQQVEALQGQVQHLQAAFSQYKKVELFPNGQSVGEKIFKTAGFVKPFTEAQLLCTQAGGQLASPRSAAENAALQQLVVAKNEAAFLSMTDSKTEGKFTYPTGESLVYSNWAPGEPNDDGGSEDCVEIFTNGKWNDRACGEKRLVVCEF

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 branched

描述 description	alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
分子量 formula_weight	504.4 kDa
来源方法 src_method	man
拷贝数 entity_count	3

Entity 3 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	9

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	275

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6. 折叠分类 (SCOP + CATH) 9 domains

SCOP 2.08 (6 domains)

结构域编号 domain_id	d2ggua1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.169 — C-type lectin-like
超家族 Superfamily superfamily	d.169.1 — C-type lectin-like
家族 Family family	d.169.1.1 — C-type lectin domain

结构域编号 domain_id	d2ggua2
类 Class class	h — Coiled coil proteins
折叠类型 Fold fold	h.1 — Parallel coiled-coil
超家族 Superfamily superfamily	h.1.1 — Triple coiled coil domain of C-type lectins
家族 Family family	h.1.1.1 — Triple coiled coil domain of C-type lectins

结构域编号 domain_id	d2ggub1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.169 — C-type lectin-like
超家族 Superfamily superfamily	d.169.1 — C-type lectin-like
家族 Family family	d.169.1.1 — C-type lectin domain

结构域编号 domain_id	d2ggub2
类 Class class	h — Coiled coil proteins
折叠类型 Fold fold	h.1 — Parallel coiled-coil
超家族 Superfamily superfamily	h.1.1 — Triple coiled coil domain of C-type lectins
家族 Family family	h.1.1.1 — Triple coiled coil domain of C-type lectins

结构域编号 domain_id	d2gguc1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.169 — C-type lectin-like
超家族 Superfamily superfamily	d.169.1 — C-type lectin-like
家族 Family family	d.169.1.1 — C-type lectin domain

结构域编号 domain_id	d2gguc2
类 Class class	h — Coiled coil proteins
折叠类型 Fold fold	h.1 — Parallel coiled-coil
超家族 Superfamily superfamily	h.1.1 — Triple coiled coil domain of C-type lectins
家族 Family family	h.1.1.1 — Triple coiled coil domain of C-type lectins

CATH v4.4 (3 domains)

结构域编号 domain_id	2gguA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	100 — Mannose-Binding Protein A; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Mannose-Binding Protein A, subunit A

结构域编号 domain_id	2gguB00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	100 — Mannose-Binding Protein A; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Mannose-Binding Protein A, subunit A

结构域编号 domain_id	2gguC00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	100 — Mannose-Binding Protein A; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Mannose-Binding Protein A, subunit A

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7. 引用文献 (1)

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晶胞边长 a length_a	55.730 Å
晶胞边长 b length_b	108.930 Å
晶胞边长 c length_c	55.840 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	91.12 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	6

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	1.900 Å
最低分辨率 resolution_low	50.000 Å
R 因子 r_factor	0.2250
R_work r_work	0.2210
R_free r_free	0.2480

fit	/app/data/saxs_computation/gg/2ggu/2ggu.fit
pddf	/app/data/pr_computation/gg/2ggu/2ggu.pr.out
profile	/app/data/saxs_computation/gg/2ggu/2ggu.dat

;crystal structure of the trimeric neck and carbohydrate recognition domain of human surfactant protein D in complex with maltotriose ;

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

来源 Source

Entity 2 branched

Entity 3 non-polymer

Entity 4 water

6. 折叠分类 (SCOP + CATH) 9 domains

SCOP 2.08 (6 domains)

CATH v4.4 (3 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)