SAXSdb — 1nod

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1nod
沉积日期 deposition_date	1998-03-05
结构标题 title	MURINE INDUCIBLE NITRIC OXIDE SYNTHASE OXYGENASE DIMER (DELTA 65) WITH TETRAHYDROBIOPTERIN AND SUBSTRATE L-ARGININE
关键词 keywords	;NITRIC OXIDE L-ARGININE MONOOXYGENASE, HEME, DIMER, NOS, COMPLEX (OXIDOREDUCTASE-SUBSTRATE), COMPLEX (OXIDOREDUCTASE-SUBSTRATE) complex ;; COMPLEX (OXIDOREDUCTASE/SUBSTRATE)
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	35.87 Å
回转半径 Rg (电子) rg_electron	35.49 Å
零角强度 I(0) i0	146349000.00
分子量 molecular_weight	97699.0 kDa
排除体积 excluded_volume	122240 Å³
包络体积 envelope_volume	162190 Å³
水化壳体积 shell_volume	38795 Å³
包络直径 envelope_diameter	123.8 Å
壳层 Rg shell_rg	40.93 Å
包络 Rg envelope_rg	35.02 Å
形状 Rg shape_rg	35.46 Å
总 Rg total_rg	35.99 Å
总原子数 total_atoms	6890
残基数 n_residues	827
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	115.7 Å
Rg (实空间) rg_real	35.95 Å
Rg 误差 (实空间) rg_real_error	1.37 Å
I(0) (实空间) i0_real	1.4630e+08
I(0) 误差 (实空间) i0_real_error	2.5830e+06
Rg (倒空间) rg_reciprocal	35.90 Å
I(0) (倒空间) i0_reciprocal	146300000.0000
解质量估计 total_estimate	0.8805
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	31.6 Å
偏度 Skewness skewness	0.293
峰度 Kurtosis kurtosis	-0.728
角度范围 angular_range	— – 0.2200 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	22650000.0000
实空间数据点数 n_real_points	45
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.878; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.917; Smooth: 0.893

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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	NITRIC OXIDE SYNTHASE
分子量 formula_weight	48998.7 kDa
EC 编号 ec_number	1.14.13.39
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	7208

QYVRIKNWGSGEILHDTLHHKATSDFTCKSKSCLGSIMNPKSLTRGPRDKPTPLEELLPHAIEFINQYYGSFKEAKIEEHLARLEAVTKEIETTGTYQLTLDELIFATKMAWRNAPRCIGRIQWSNLQVFDARNCSTAQEMFQHICRHILYATNNGNIRSAITVFPQRSDGKHDFRLWNSQLIRYAGYQMPDGTIRGDAATLEFTQLCIDLGWKPRYGRFDVLPLVLQADGQDPEVFEIPPDLVLEVTMEHPKYEWFQELGLKWYALPAVANMLLEVGGLEFPACPFNGWYMGTEIGVRDFCDTQRYNILEEVGRRMGLETHTLASLWKDRAVTEINVAVLHSFQKQNVTIMDHHTASESFMKHMQNEYRARGGCPADWIWLVPPVSGSITPVFHQEMLNYVLSPFYYYQIEPWKTHIWQNEK

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI 分类编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 2 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 3 non-polymer

描述 description	ARGININE
分子量 formula_weight	175.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 non-polymer

描述 description	PROTOPORPHYRIN IX CONTAINING FE
分子量 formula_weight	616.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 5 non-polymer

描述 description	5,6,7,8-TETRAHYDROBIOPTERIN
分子量 formula_weight	241.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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	318

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6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d1noda_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.174 — Nitric oxide (NO) synthase oxygenase domain
超家族 Superfamily superfamily	d.174.1 — Nitric oxide (NO) synthase oxygenase domain
家族 Family family	d.174.1.1 — Nitric oxide (NO) synthase oxygenase domain

结构域编号 domain_id	d1nodb_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.174 — Nitric oxide (NO) synthase oxygenase domain
超家族 Superfamily superfamily	d.174.1 — Nitric oxide (NO) synthase oxygenase domain
家族 Family family	d.174.1.1 — Nitric oxide (NO) synthase oxygenase domain

CATH v4.4 (6 domains)

结构域编号 domain_id	1nodA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	340 — Nitric Oxide Synthase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Nitric Oxide Synthase; Chain A, domain 1

结构域编号 domain_id	1nodA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	440 — Nitric Oxide Synthase;Heme Domain; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Nitric Oxide Synthase;Heme Domain;Chain A domain 2

结构域编号 domain_id	1nodA03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1230 — Bovine Endothelial Nitric Oxide Synthase Heme Domain; Chain: A,domain 3
同源超家族 H-superfamily homologous superfamily	10 — Nitric Oxide Synthase; Chain A, domain 3

结构域编号 domain_id	1nodB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	340 — Nitric Oxide Synthase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Nitric Oxide Synthase; Chain A, domain 1

结构域编号 domain_id	1nodB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	440 — Nitric Oxide Synthase;Heme Domain; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Nitric Oxide Synthase;Heme Domain;Chain A domain 2

结构域编号 domain_id	1nodB03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1230 — Bovine Endothelial Nitric Oxide Synthase Heme Domain; Chain: A,domain 3
同源超家族 H-superfamily homologous superfamily	10 — Nitric Oxide Synthase; Chain A, domain 3

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7. 引用文献 (3)

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晶胞边长 a length_a	213.000 Å
晶胞边长 b length_b	213.000 Å
晶胞边长 c length_c	114.200 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	24

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	2.600 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.2290
R_work r_work	0.2290
R_free r_free	0.2880

fit	/app/data/saxs_computation/no/1nod/1nod.fit
pddf	/app/data/pr_computation/no/1nod/1nod.pr.out
profile	/app/data/saxs_computation/no/1nod/1nod.dat

MURINE INDUCIBLE NITRIC OXIDE SYNTHASE OXYGENASE DIMER (DELTA 65) WITH TETRAHYDROBIOPTERIN AND SUBSTRATE L-ARGININE

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution