SAXSdb — 1m8e

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1m8e
沉积日期 deposition_date	2002-07-24
结构标题 title	inducible nitric oxide synthase with 7-nitroindazole bound
关键词 keywords	oxidoreductase; OXIDOREDUCTASE
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	36.24 Å
回转半径 Rg (电子) rg_electron	35.89 Å
零角强度 I(0) i0	143710000.00
分子量 molecular_weight	97193.0 kDa
排除体积 excluded_volume	121660 Å³
包络体积 envelope_volume	162180 Å³
水化壳体积 shell_volume	38169 Å³
包络直径 envelope_diameter	123.9 Å
壳层 Rg shell_rg	41.53 Å
包络 Rg envelope_rg	35.32 Å
形状 Rg shape_rg	35.86 Å
总 Rg total_rg	36.39 Å
总原子数 total_atoms	6858
残基数 n_residues	823
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	116.9 Å
Rg (实空间) rg_real	36.34 Å
Rg 误差 (实空间) rg_real_error	1.18 Å
I(0) (实空间) i0_real	1.4370e+08
I(0) 误差 (实空间) i0_real_error	2.3490e+06
Rg (倒空间) rg_reciprocal	36.28 Å
I(0) (倒空间) i0_reciprocal	143700000.0000
解质量估计 total_estimate	0.8757
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	31.9 Å
偏度 Skewness skewness	0.283
峰度 Kurtosis kurtosis	-0.760
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	21800000.0000
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: 0.866; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.900; Smooth: 0.885

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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	inducible Nitric oxide synthase
分子量 formula_weight	50208.0 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	7050

SLDKLHVTSTRPQYVRIKNWGSGEILHDTLHHKATSDFTCKSKSCLGSIMNPKSLTRGPRDKPTPLEELLPHAIEFINQYYGSFKEAKIEEHLARLEAVTKEIETTGTYQLTLDELIFATKMAWRNAPRCIGRIQWSNLQVFDARNCSTAQEMFQHICRHILYATNNGNIRSAITVFPQRSDGKHDFRLWNSQLIRYAGYQMPDGTIRGDAATLEFTQLCIDLGWKPRYGRFDVLPLVLQADGQDPEVFEIPPDLVLEVTMEHPKYEWFQELGLKWYALPAVANMLLEVGGLEFPACPFNGWYMGTEIGVRDFCDTQRYNILEEVGRRMGLETHTLASLWKDRAVTEINVAVLHSFQKQNVTIMDHHTASESFMKHMQNEYRARGGCPADWIWLVPPVSGSITPVFHQEMLNYVLSPFYYYQIEPWKTHIWQNE

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	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 3 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 4 non-polymer

描述 description	7-NITROINDAZOLE
分子量 formula_weight	163.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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	168

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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	d1m8ea_
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	d1m8eb_
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	1m8eA01
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	1m8eA02
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	1m8eA03
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	1m8eB01
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	1m8eB02
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	1m8eB03
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 (2)

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晶胞边长 a length_a	213.067 Å
晶胞边长 b length_b	213.067 Å
晶胞边长 c length_c	115.783 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	2.900 Å
最低分辨率 resolution_low	19.910 Å
R 因子 r_factor	—
R_work r_work	0.2350
R_free r_free	0.2800

fit	/app/data/saxs_computation/m8/1m8e/1m8e.fit
pddf	/app/data/pr_computation/m8/1m8e/1m8e.pr.out
profile	/app/data/saxs_computation/m8/1m8e/1m8e.dat

inducible nitric oxide synthase with 7-nitroindazole bound

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