SAXSdb — 2jdm

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2jdm
沉积日期 deposition_date	2007-01-11
结构标题 title	Mutant (S22A) of Pseudomonas aeruginosa lectin II (PA-IIL) complexed with methyl-a-L-fucopyranoside
关键词 keywords	ECTIN, GLYCOMIMETIC, CYSTIC FIBROSIS, 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	22.58 Å
回转半径 Rg (电子) rg_electron	21.07 Å
零角强度 I(0) i0	41917800.00
分子量 molecular_weight	48055.0 kDa
排除体积 excluded_volume	59225 Å³
包络体积 envelope_volume	67352 Å³
水化壳体积 shell_volume	25919 Å³
包络直径 envelope_diameter	67.5 Å
壳层 Rg shell_rg	28.31 Å
包络 Rg envelope_rg	21.14 Å
形状 Rg shape_rg	21.02 Å
总 Rg total_rg	22.00 Å
总原子数 total_atoms	3369
残基数 n_residues	456
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	68.3 Å
Rg (实空间) rg_real	22.40 Å
Rg 误差 (实空间) rg_real_error	0.50 Å
I(0) (实空间) i0_real	4.1920e+07
I(0) 误差 (实空间) i0_real_error	5.9420e+05
Rg (倒空间) rg_reciprocal	22.44 Å
I(0) (倒空间) i0_reciprocal	41920000.0000
解质量估计 total_estimate	0.9017
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	30.0 Å
偏度 Skewness skewness	0.008
峰度 Kurtosis kurtosis	-0.533
角度范围 angular_range	— – 0.3500 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	5028000.0000
实空间数据点数 n_real_points	67
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.916; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.995

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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 (6)

Entity 1 polymer

描述 description	FUCOSE-BINDING LECTIN PA-IIL
分子量 formula_weight	11849.9 kDa
突变 mutation	YES
来源方法 src_method	man
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	3950

MATQGVFTLPANTRFGVTAFANASGTQTVNVLVNNETAATFSGQSTNNAVIGTQVLNSGSSGKVQVQVSVNGRPSDLVSAQVILTNELNFALVGSEDGTDNDYNDAVVVINWPLG

来源 Source

来源生物 organism	PSEUDOMONAS AERUGINOSA
NCBI 分类编号 ncbi_taxonomy_id	287
宿主生物 host_organism	ESCHERICHIA COLI

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	8

Entity 3 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	2

Entity 4 non-polymer

描述 description	alpha-L-fucopyranose
分子量 formula_weight	164.2 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 5 non-polymer

描述 description	methyl alpha-L-fucopyranoside
分子量 formula_weight	178.2 kDa
来源方法 src_method	man
拷贝数 entity_count	3

Entity 6 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	524

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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	d2jdma_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.115 — Calcium-mediated lectin
超家族 Superfamily superfamily	b.115.1 — Calcium-mediated lectin
家族 Family family	b.115.1.1 — Calcium-mediated lectin

结构域编号 domain_id	d2jdmb_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.115 — Calcium-mediated lectin
超家族 Superfamily superfamily	b.115.1 — Calcium-mediated lectin
家族 Family family	b.115.1.1 — Calcium-mediated lectin

结构域编号 domain_id	d2jdmc_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.115 — Calcium-mediated lectin
超家族 Superfamily superfamily	b.115.1 — Calcium-mediated lectin
家族 Family family	b.115.1.1 — Calcium-mediated lectin

结构域编号 domain_id	d2jdmd_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.115 — Calcium-mediated lectin
超家族 Superfamily superfamily	b.115.1 — Calcium-mediated lectin
家族 Family family	b.115.1.1 — Calcium-mediated lectin

CATH v4.4 (4 domains)

结构域编号 domain_id	2jdmA00
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	400 — Calcium-mediated lectin

结构域编号 domain_id	2jdmB00
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	400 — Calcium-mediated lectin

结构域编号 domain_id	2jdmC00
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	400 — Calcium-mediated lectin

结构域编号 domain_id	2jdmD00
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	400 — Calcium-mediated lectin

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7. 引用文献 (5)

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晶胞边长 a length_a	52.674 Å
晶胞边长 b length_b	73.090 Å
晶胞边长 c length_c	54.917 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	94.25 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

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	1.700 Å
最低分辨率 resolution_low	54.800 Å
R 因子 r_factor	0.1770
R_work r_work	0.1740
R_free r_free	0.2230

fit	/app/data/saxs_computation/jd/2jdm/2jdm.fit
pddf	/app/data/pr_computation/jd/2jdm/2jdm.pr.out
profile	/app/data/saxs_computation/jd/2jdm/2jdm.dat

Mutant (S22A) of Pseudomonas aeruginosa lectin II (PA-IIL) complexed with methyl-a-L-fucopyranoside

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 (6)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 non-polymer

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 water

6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. 引用文献 (5)

8. 文件与曲线 (10)

Files (7)

Curves (3)