SAXSdb — 1fj0

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1fj0
沉积日期 deposition_date	2000-08-07
结构标题 title	STRUCTURE DETERMINATION OF THE FERRICYTOCHROME C2 FROM RHODOPSEUDOMONAS PALUSTRIS
关键词 keywords	ELECTRON CARRIER, HEME PROTEIN, ELECTRON TRANSPORT; ELECTRON TRANSPORT
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	26.47 Å
回转半径 Rg (电子) rg_electron	25.48 Å
零角强度 I(0) i0	43188700.00
分子量 molecular_weight	51459.0 kDa
排除体积 excluded_volume	64640 Å³
包络体积 envelope_volume	78407 Å³
水化壳体积 shell_volume	25730 Å³
包络直径 envelope_diameter	81.1 Å
壳层 Rg shell_rg	32.74 Å
包络 Rg envelope_rg	24.78 Å
形状 Rg shape_rg	25.46 Å
总 Rg total_rg	26.41 Å
总原子数 total_atoms	3608
残基数 n_residues	452
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	79.4 Å
Rg (实空间) rg_real	26.36 Å
Rg 误差 (实空间) rg_real_error	0.58 Å
I(0) (实空间) i0_real	4.3190e+07
I(0) 误差 (实空间) i0_real_error	6.3690e+05
Rg (倒空间) rg_reciprocal	26.40 Å
I(0) (倒空间) i0_reciprocal	43190000.0000
解质量估计 total_estimate	0.9175
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	38.4 Å
偏度 Skewness skewness	0.105
峰度 Kurtosis kurtosis	-0.658
角度范围 angular_range	— – 0.3000 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	6735000.0000
实空间数据点数 n_real_points	61
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.981; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.988

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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	CYTOCHROME C2
分子量 formula_weight	12187.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	4264

QDAKAGEAVFKQCMTCHRADKNMVGPALAGVVGRKAGTAAGFTYSPLNHNSGEAGLVWTADNIVPYLADPNAFLKKFLTEKGKADQAVGVTKMTFKLANEQQRKDVVAYLATLK

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	HEME C
分子量 formula_weight	618.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

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	1

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	653

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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	d1fj0a_
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.3.1.1 — monodomain cytochrome c

结构域编号 domain_id	d1fj0b_
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.3.1.1 — monodomain cytochrome c

结构域编号 domain_id	d1fj0c_
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.3.1.1 — monodomain cytochrome c

结构域编号 domain_id	d1fj0d_
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.3.1.1 — monodomain cytochrome c

CATH v4.4 (4 domains)

结构域编号 domain_id	1fj0A00
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	1fj0B00
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	1fj0C00
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	1fj0D00
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

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7. 引用文献 (4)

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晶胞边长 a length_a	50.310 Å
晶胞边长 b length_b	71.530 Å
晶胞边长 c length_c	66.660 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	93.52 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

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	1.700 Å
最低分辨率 resolution_low	50.000 Å
R 因子 r_factor	—
R_work r_work	0.1777
R_free r_free	0.2179

fit	/app/data/saxs_computation/fj/1fj0/1fj0.fit
pddf	/app/data/pr_computation/fj/1fj0/1fj0.pr.out
profile	/app/data/saxs_computation/fj/1fj0/1fj0.dat

STRUCTURE DETERMINATION OF THE FERRICYTOCHROME C2 FROM RHODOPSEUDOMONAS PALUSTRIS

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

5. 实体与聚合体信息 (5)

Entity 1 polymer

聚合体 Polymer

Entity 2 non-polymer

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 water

6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. 引用文献 (4)

8. 文件与曲线 (10)

Files (7)

Curves (3)