SAXSdb — 1jdn

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1jdn
沉积日期 deposition_date	2001-06-14
结构标题 title	Crystal Structure of Hormone Receptor
关键词 keywords	Natriuretic peptide receptor, dimer, allosteric activation, SIGNALING PROTEIN; SIGNALING 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	23.43 Å
回转半径 Rg (电子) rg_electron	22.39 Å
零角强度 I(0) i0	39036200.00
分子量 molecular_weight	47839.0 kDa
排除体积 excluded_volume	59614 Å³
包络体积 envelope_volume	70243 Å³
水化壳体积 shell_volume	25992 Å³
包络直径 envelope_diameter	80.2 Å
壳层 Rg shell_rg	29.58 Å
包络 Rg envelope_rg	22.69 Å
形状 Rg shape_rg	22.38 Å
总 Rg total_rg	23.24 Å
总原子数 total_atoms	3364
残基数 n_residues	407
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	76.0 Å
Rg (实空间) rg_real	23.38 Å
Rg 误差 (实空间) rg_real_error	0.53 Å
I(0) (实空间) i0_real	3.9040e+07
I(0) 误差 (实空间) i0_real_error	5.4640e+05
Rg (倒空间) rg_reciprocal	23.39 Å
I(0) (倒空间) i0_reciprocal	39040000.0000
解质量估计 total_estimate	0.6030
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	28.0 Å
偏度 Skewness skewness	0.345
峰度 Kurtosis kurtosis	-0.262
角度范围 angular_range	— – 0.3400 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	8963000.0000
实空间数据点数 n_real_points	66
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.831; Stabil: 0.999; Sysdev: 0.115; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

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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	ATRIAL NATRIURETIC PEPTIDE CLEARANCE RECEPTOR
分子量 formula_weight	49541.8 kDa
来源方法 src_method	man
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	3364

EREALPPQKIEVLVLLPQDDSYLFSLTRVRPAIEYALRSVEGNGTGRRLLPPGTRFQVAYEDSDCGNRALFSLVDRVAAARGAKPDLILGPVCEYAAAPVARLASHWDLPMLSAGALAAGFQHKDSEYSHLTRVAPAYAKMGEMMLALFRHHHWSRAALVYSDDKLERNCYFTLEGVHEVFQEEGLHTSIYSFDETKDLDLEDIVRNIQASERVVIMCASSDTIRSIMLVAHRHGMTSGDYAFFNIELFNSSSYGDGSWKRGDKHDFEAKQAYSSLQTVTLLRTVKPEFEKFSMEVKSSVEKQGLNMEDYVNMFVEGFHDAILLYVLALHEVLRAGYSKKDGGKIIQQTWNRTFEGIAGQVSIDANGDRYGDFSVIAMTDVEAGTQEVIGDYFGKEGRFEMRPNVKYPWGPLKLRIDENRIVEHTNSSPCKSCGLEESAVT

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	Drosophila melanogaster

Entity 2 branched

描述 description	;beta-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-4)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-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 3 branched

描述 description	;beta-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	894.8 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 4 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	2

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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	d1jdna_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.93 — Periplasmic binding protein-like I
超家族 Superfamily superfamily	c.93.1 — Periplasmic binding protein-like I
家族 Family family	c.93.1.1 — L-arabinose binding protein-like

CATH v4.4 (2 domains)

结构域编号 domain_id	1jdnA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	2300 — Response regulator

结构域编号 domain_id	1jdnA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	2300 — Response regulator

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7. 引用文献 (1)

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晶胞边长 a length_a	217.189 Å
晶胞边长 b length_b	217.189 Å
晶胞边长 c length_c	130.793 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	120.00 °
晶胞分子数 Z z_pdb	12

空间群 space_group	P 61 2 2
空间群编号 int_tables_number	178
晶系 crystal_system	—

分辨率 resolution	2.900 Å
最低分辨率 resolution_low	50.000 Å
R 因子 r_factor	—
R_work r_work	0.2430
R_free r_free	0.2560

fit	/app/data/saxs_computation/jd/1jdn/1jdn.fit
pddf	/app/data/pr_computation/jd/1jdn/1jdn.pr.out
profile	/app/data/saxs_computation/jd/1jdn/1jdn.dat

Crystal Structure of Hormone Receptor

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