1i6d

SOLUTION STRUCTURE OF THE FUNCTIONAL DOMAIN OF PARACOCCUS DENITRIFICANS CYTOCHROME C552 IN THE REDUCED STATE

Method: SOLUTION NMR D_max: 39.5 Å Quality: REASONABLE

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

下载 Download SAXS (.dat) P(r) (.pr.out) CIF

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1i6d
沉积日期 deposition_date	2001-03-02
结构标题 title	SOLUTION STRUCTURE OF THE FUNCTIONAL DOMAIN OF PARACOCCUS DENITRIFICANS CYTOCHROME C552 IN THE REDUCED STATE
关键词 keywords	ELECTRON TRANSPORT, CYTOCHROME C552, HEME, REDOX STATES, ISOTOPE ENRICHMENT {13C/15N}, NMR SPECTROSCOPY, SOLUTION STRUCTURE; ELECTRON TRANSPORT
实验方法 method	SOLUTION NMR

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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	12.75 Å
回转半径 Rg (电子) rg_electron	12.44 Å
零角强度 I(0) i0	695797000.00
分子量 molecular_weight	223150.0 kDa
排除体积 excluded_volume	278310 Å³
包络体积 envelope_volume	19004 Å³
水化壳体积 shell_volume	11986 Å³
包络直径 envelope_diameter	44.6 Å
壳层 Rg shell_rg	19.27 Å
包络 Rg envelope_rg	13.72 Å
形状 Rg shape_rg	12.41 Å
总 Rg total_rg	12.67 Å
总原子数 total_atoms	30600
残基数 n_residues	2000
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	39.5 Å
Rg (实空间) rg_real	12.64 Å
Rg 误差 (实空间) rg_real_error	0.24 Å
I(0) (实空间) i0_real	6.9580e+08
I(0) 误差 (实空间) i0_real_error	8.3950e+06
Rg (倒空间) rg_reciprocal	12.65 Å
I(0) (倒空间) i0_reciprocal	695800000.0000
解质量估计 total_estimate	0.7413
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	17.0 Å
偏度 Skewness skewness	0.022
峰度 Kurtosis kurtosis	-0.340
角度范围 angular_range	— – 0.5000 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	192600.0000
实空间数据点数 n_real_points	80
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.856; Stabil: 1.000; Sysdev: 0.368; Positv: 1.000; Valcen: 0.983; Smooth: 0.977

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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 (2)

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6. 折叠分类 (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

结构域编号 domain_id	d1i6da_
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 (1 domains)

结构域编号 domain_id	1i6dA00
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	1.000 Å
晶胞边长 b length_b	1.000 Å
晶胞边长 c length_c	1.000 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	1

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

描述 description	CYTOCHROME C552
分子量 formula_weight	10554.0 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	30600

来源生物 organism	Paracoccus denitrificans
NCBI 分类编号 ncbi_taxonomy_id	266
宿主生物 host_organism	Escherichia coli BL21(DE3)

SOLUTION STRUCTURE OF THE FUNCTIONAL DOMAIN OF PARACOCCUS DENITRIFICANS CYTOCHROME C552 IN THE REDUCED STATE

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

5. 实体与聚合体信息 (2)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 non-polymer

6. 折叠分类 (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. 引用文献 (4)

8. 文件与曲线 (10)

Files (7)

Curves (3)

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	1

fit	/app/data/saxs_computation/i6/1i6d/1i6d.fit
pddf	/app/data/pr_computation/i6/1i6d/1i6d.pr.out
profile	/app/data/saxs_computation/i6/1i6d/1i6d.dat