SAXSdb — 1rtm

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1rtm
沉积日期 deposition_date	1994-11-21
结构标题 title	TRIMERIC STRUCTURE OF A C-TYPE MANNOSE-BINDING PROTEIN
关键词 keywords	LECTIN; LECTIN
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	27.06 Å
回转半径 Rg (电子) rg_electron	26.04 Å
零角强度 I(0) i0	45646900.00
分子量 molecular_weight	51213.0 kDa
排除体积 excluded_volume	63644 Å³
包络体积 envelope_volume	77695 Å³
水化壳体积 shell_volume	26079 Å³
包络直径 envelope_diameter	82.7 Å
壳层 Rg shell_rg	31.95 Å
包络 Rg envelope_rg	26.09 Å
形状 Rg shape_rg	25.99 Å
总 Rg total_rg	26.85 Å
总原子数 total_atoms	3561
残基数 n_residues	447
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	79.2 Å
Rg (实空间) rg_real	26.93 Å
Rg 误差 (实空间) rg_real_error	0.44 Å
I(0) (实空间) i0_real	4.5650e+07
I(0) 误差 (实空间) i0_real_error	5.9420e+05
Rg (倒空间) rg_reciprocal	26.97 Å
I(0) (倒空间) i0_reciprocal	45650000.0000
解质量估计 total_estimate	0.9155
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	40.3 Å
偏度 Skewness skewness	0.039
峰度 Kurtosis kurtosis	-0.783
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	11180000.0000
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: 0.979; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.967

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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	MANNOSE-BINDING PROTEIN-A
分子量 formula_weight	16478.7 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	1,2,3
原子数 atom_count	4061

AIEVKLANMEAEINTLKSKLELTNKLHAFSMGKKSGKKFFVTNHERMPFSKVKALCSELRGTVAIPRNAEENKAIQEVAKTSAFLGITDEVTEGQFMYVTGGRLTYSNWKKDEPNDHGSGEDCVTIVDNGLWNDISCQASHTAVCEFPA

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	Norway rat
NCBI 分类编号 ncbi_taxonomy_id	10116

Entity 2 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 3 non-polymer

描述 description	CHLORIDE ION
分子量 formula_weight	35.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 4 non-polymer

描述 description	GLYCEROL
分子量 formula_weight	92.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	15

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	475

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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	d1rtm11
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	d1rtm12
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	d1rtm21
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	d1rtm22
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	d1rtm31
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	d1rtm32
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	1rtm100
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	1rtm200
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	1rtm300
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 (4)

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晶胞边长 a length_a	80.000 Å
晶胞边长 b length_b	85.100 Å
晶胞边长 c length_c	98.500 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	106.30 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	12

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	—

分辨率 resolution	1.800 Å
最低分辨率 resolution_low	10.000 Å
R 因子 r_factor	0.2200
R_work r_work	0.2200
R_free r_free	0.2700

fit	/app/data/saxs_computation/rt/1rtm/1rtm.fit
pddf	/app/data/pr_computation/rt/1rtm/1rtm.pr.out
profile	/app/data/saxs_computation/rt/1rtm/1rtm.dat

TRIMERIC STRUCTURE OF A C-TYPE MANNOSE-BINDING PROTEIN

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

5. 实体与聚合体信息 (5)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 non-polymer

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 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 (4)

8. 文件与曲线 (10)

Files (7)

Curves (3)