SAXSdb — 1nno

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1nno
沉积日期 deposition_date	1998-07-20
结构标题 title	CONFORMATIONAL CHANGES OCCURRING UPON NO BINDING IN NITRITE REDUCTASE FROM PSEUDOMONAS AERUGINOSA
关键词 keywords	NITRITE REDUCTASE, PSEUDOMONAS AERUGINOSA, HEMOPROTEIN, DENITRIFICATION, NO BINDING, CONFORMATIONAL CHANGES, 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	33.13 Å
回转半径 Rg (电子) rg_electron	32.68 Å
零角强度 I(0) i0	228048000.00
分子量 molecular_weight	122100.0 kDa
排除体积 excluded_volume	152960 Å³
包络体积 envelope_volume	182700 Å³
水化壳体积 shell_volume	46039 Å³
包络直径 envelope_diameter	113.3 Å
壳层 Rg shell_rg	39.99 Å
包络 Rg envelope_rg	32.86 Å
形状 Rg shape_rg	32.67 Å
总 Rg total_rg	33.24 Å
总原子数 total_atoms	8614
残基数 n_residues	1078
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	108.5 Å
Rg (实空间) rg_real	33.14 Å
Rg 误差 (实空间) rg_real_error	0.60 Å
I(0) (实空间) i0_real	2.2800e+08
I(0) 误差 (实空间) i0_real_error	3.5330e+06
Rg (倒空间) rg_reciprocal	33.14 Å
I(0) (倒空间) i0_reciprocal	228000000.0000
解质量估计 total_estimate	0.8874
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	36.1 Å
偏度 Skewness skewness	0.350
峰度 Kurtosis kurtosis	-0.427
角度范围 angular_range	— – 0.2400 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	72340000.0000
实空间数据点数 n_real_points	49
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.887; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.883

▶

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

▶

5. 实体与聚合体信息 (5)

Entity 1 polymer

描述 description	NITRITE REDUCTASE
分子量 formula_weight	60259.1 kDa
EC 编号 ec_number	1.9.3.2
来源方法 src_method	nat
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	8968

KDDMKAAEQYQGAASAVDPAHVVRTNGAPDMSESEFNEAKQIYFQRCAGCHGVLRKGATGKPLTPDITQQRGQQYLEALITYGTPLGMPNWGSSGELSKEQITLMAKYIQHTPPQPPEWGMPEMRESWKVLVKPEDRPKKQLNDLDLPNLFSVTLRDAGQIALVDGDSKKIVKVIDTGYAVHISRMSASGRYLLVIGRDARIDMIDLWAKEPTKVAEIKIGIEARSVESSKFKGYEDRYTIAGAYWPPQFAIMDGETLEPKQIVSTRGMTVDTQTYHPEPRVAAIIASHEHPEFIVNVKETGKVLLVNYKDIDNLTVTSIGAAPFLHDGGWDSSHRYFMTAANNSNKVAVIDSKDRRLSALVDVGKTPHPGRGANFVHPKYGPVWSTSHLGDGSISLIGTDPKNHPQYAWKKVAELQGQGGGSLFIKTHPKSSHLYVDTTFNPDARISQSVAVFDLKNLDAKYQVLPIAEWADLGEGAKRVVQPEYNKRGDEVWFSVWNGKNDSSALVVVDDKTLKLKAVVKDPRLITPTGKFNVYNTQHDVY

Entity 2 non-polymer

描述 description	HEME C
分子量 formula_weight	618.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 3 non-polymer

描述 description	HEME D
分子量 formula_weight	712.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 non-polymer

描述 description	NITRIC OXIDE
分子量 formula_weight	30.0 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	354

▼

6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1nnoa1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.3 — Cytochrome c
超家族 Superfamily superfamily	a.3.1 — Cytochrome c
家族 Family family	a.3.1.2 — N-terminal (heme c) domain of cytochrome cd1-nitrite reductase

结构域编号 domain_id	d1nnoa2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.70 — 8-bladed beta-propeller
超家族 Superfamily superfamily	b.70.2 — C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase
家族 Family family	b.70.2.1 — C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase

结构域编号 domain_id	d1nnob1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.3 — Cytochrome c
超家族 Superfamily superfamily	a.3.1 — Cytochrome c
家族 Family family	a.3.1.2 — N-terminal (heme c) domain of cytochrome cd1-nitrite reductase

结构域编号 domain_id	d1nnob2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.70 — 8-bladed beta-propeller
超家族 Superfamily superfamily	b.70.2 — C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase
家族 Family family	b.70.2.1 — C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase

CATH v4.4 (4 domains)

结构域编号 domain_id	1nnoA01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	760 — Cytochrome Bc1 Complex; Chain D, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Cytochrome c-like domain

结构域编号 domain_id	1nnoA02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	140 — 8 Propeller
拓扑 Topology topology	10 — Methanol Dehydrogenase; Chain A
同源超家族 H-superfamily homologous superfamily	20 — C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase

结构域编号 domain_id	1nnoB01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	760 — Cytochrome Bc1 Complex; Chain D, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Cytochrome c-like domain

结构域编号 domain_id	1nnoB02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	140 — 8 Propeller
拓扑 Topology topology	10 — Methanol Dehydrogenase; Chain A
同源超家族 H-superfamily homologous superfamily	20 — C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	166.072 Å
晶胞边长 b length_b	88.110 Å
晶胞边长 c length_c	113.981 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	90.00 °
晶胞分子数 Z z_pdb	8

空间群 space_group	P 21 21 2
空间群编号 int_tables_number	18
晶系 crystal_system	—

分辨率 resolution	2.650 Å
最低分辨率 resolution_low	15.000 Å
R 因子 r_factor	0.2090
R_work r_work	0.2090
R_free r_free	0.2430

fit	/app/data/saxs_computation/nn/1nno/1nno.fit
pddf	/app/data/pr_computation/nn/1nno/1nno.pr.out
profile	/app/data/saxs_computation/nn/1nno/1nno.dat

CONFORMATIONAL CHANGES OCCURRING UPON NO BINDING IN NITRITE REDUCTASE FROM PSEUDOMONAS AERUGINOSA

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