SAXSdb — 1m8d

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1m8d
沉积日期 deposition_date	2002-07-24
结构标题 title	inducible nitric oxide synthase with Chlorzoxazone bound
关键词 keywords	inhibitor-induced conformational change, OXIDOREDUCTASE; OXIDOREDUCTASE
实验方法 method	X-RAY DIFFRACTION

▼

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	37.48 Å
回转半径 Rg (电子) rg_electron	37.26 Å
零角强度 I(0) i0	145847000.00
分子量 molecular_weight	98190.0 kDa
排除体积 excluded_volume	122840 Å³
包络体积 envelope_volume	162350 Å³
水化壳体积 shell_volume	37064 Å³
包络直径 envelope_diameter	127.1 Å
壳层 Rg shell_rg	42.15 Å
包络 Rg envelope_rg	36.94 Å
形状 Rg shape_rg	37.23 Å
总 Rg total_rg	37.70 Å
总原子数 total_atoms	6921
残基数 n_residues	829
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

▼

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	122.7 Å
Rg (实空间) rg_real	37.70 Å
Rg 误差 (实空间) rg_real_error	1.23 Å
I(0) (实空间) i0_real	1.4580e+08
I(0) 误差 (实空间) i0_real_error	2.7110e+06
Rg (倒空间) rg_reciprocal	37.57 Å
I(0) (倒空间) i0_reciprocal	145800000.0000
解质量估计 total_estimate	0.8480
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	32.1 Å
偏度 Skewness skewness	0.339
峰度 Kurtosis kurtosis	-0.746
角度范围 angular_range	— – 0.2100 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	22880000.0000
实空间数据点数 n_real_points	43
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.810; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.849; Smooth: 0.742

▶

4. 晶体学与实验 4. Crystallography & Experiment

▶

5. 实体与聚合体信息 (8)

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	7253

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	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 3 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 4 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 5 non-polymer

描述 description	CHLORZOXAZONE
分子量 formula_weight	169.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 6 non-polymer

描述 description	octyl beta-D-glucopyranoside
分子量 formula_weight	292.4 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 7 non-polymer

描述 description	1,2-ETHANEDIOL
分子量 formula_weight	62.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 8 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	332

▼

6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d1m8da_
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	d1m8db_
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	1m8dA01
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	1m8dA02
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	1m8dA03
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	1m8dB01
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	1m8dB02
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	1m8dB03
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

▶

7. 引用文献 (2)

▶

晶胞边长 a length_a	213.891 Å
晶胞边长 b length_b	213.891 Å
晶胞边长 c length_c	115.484 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	2.350 Å
最低分辨率 resolution_low	19.840 Å
R 因子 r_factor	—
R_work r_work	0.2380
R_free r_free	0.2680

fit	/app/data/saxs_computation/m8/1m8d/1m8d.fit
pddf	/app/data/pr_computation/m8/1m8d/1m8d.pr.out
profile	/app/data/saxs_computation/m8/1m8d/1m8d.dat

inducible nitric oxide synthase with Chlorzoxazone bound

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution