SAXSdb — 1hj3

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1hj3
沉积日期 deposition_date	2001-01-08
结构标题 title	Cytochrome cd1 Nitrite Reductase, dioxygen complex
关键词 keywords	ENZYME, NITRITE REDUCTASE, 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	33.18 Å
回转半径 Rg (电子) rg_electron	32.56 Å
零角强度 I(0) i0	236775000.00
分子量 molecular_weight	122840.0 kDa
排除体积 excluded_volume	152960 Å³
包络体积 envelope_volume	180880 Å³
水化壳体积 shell_volume	45874 Å³
包络直径 envelope_diameter	110.7 Å
壳层 Rg shell_rg	39.81 Å
包络 Rg envelope_rg	32.64 Å
形状 Rg shape_rg	32.58 Å
总 Rg total_rg	33.01 Å
总原子数 total_atoms	8658
残基数 n_residues	1086
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	108.6 Å
Rg (实空间) rg_real	33.17 Å
Rg 误差 (实空间) rg_real_error	0.88 Å
I(0) (实空间) i0_real	2.3680e+08
I(0) 误差 (实空间) i0_real_error	3.1450e+06
Rg (倒空间) rg_reciprocal	33.18 Å
I(0) (倒空间) i0_reciprocal	236800000.0000
解质量估计 total_estimate	0.8899
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	36.2 Å
偏度 Skewness skewness	0.334
峰度 Kurtosis kurtosis	-0.450
角度范围 angular_range	— – 0.2400 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	68190000.0000
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: 0.885; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.919

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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 (7)

Entity 1 polymer

描述 description	Nitrite reductase
分子量 formula_weight	62546.5 kDa
EC 编号 ec_number	1.7.2.1,1.7.99.1
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	9453

QEQVAPPKDPAAALEDHKTRTDNRYEPSLDNLAQQDVAAPGAPEGVSALSDAQYNEANKIYFERCAGCHGVLRKGATGKALTPDLTRDLGFDYLQSFITYGSPAGMPNWGTSGELSAEQVDLMANYLLLDPAAPPEFGMKEMRESWKVHVAPEDRPTQQENDWDLENLFSVTLRDAGQIALIDGATYEIKSVLDTGYAVHISRLSASGRYLFVIGRDGKVNMIDLWMKEPTTVAEIKIGSEARSIETSKMEGWEDKYAIAGAYWPPQYVIMDGETLEPKKIQSTRGMTYDEQEYHPEPRVAAILASHYRPEFIVNVKETGKILLVDYTDLDNLKTTEISAERFLHDGGLDGSHRYFITAANARNKLVVIDTKEGKLVAIEDTGGQTPHPGRGANFVHPTFGPVWATSHMGDDSVALIGTDPEGHPDNAWKILDSFPALGGGSLFIKTHPNSQYLYVDATLNPEAEISGSVAVFDIKAMTGDGSDPEFKTLPIAEWAGITEGQPRVVQGEFNKDGTEVWFSVWNGKDQESALVVVDDKTLELKHVIKDERLVTPTGKFNVYNTMTDTY

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	GLYCEROL
分子量 formula_weight	92.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 5 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	3

Entity 6 non-polymer

描述 description	OXYGEN MOLECULE
分子量 formula_weight	32.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 7 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	795

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6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1hj3a1
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	d1hj3a2
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	d1hj3b1
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	d1hj3b2
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	1hj3A01
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	1hj3A02
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	1hj3B01
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	1hj3B02
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

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7. 引用文献 (3)

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晶胞边长 a length_a	107.190 Å
晶胞边长 b length_b	61.170 Å
晶胞边长 c length_c	100.520 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	112.19 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	—

分辨率 resolution	1.600 Å
最低分辨率 resolution_low	30.000 Å
R 因子 r_factor	—
R_work r_work	0.1960
R_free r_free	0.2190

fit	/app/data/saxs_computation/hj/1hj3/1hj3.fit
pddf	/app/data/pr_computation/hj/1hj3/1hj3.pr.out
profile	/app/data/saxs_computation/hj/1hj3/1hj3.dat

Cytochrome cd1 Nitrite Reductase, dioxygen complex

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution