SAXSdb — 1s6v

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1s6v
沉积日期 deposition_date	2004-01-27
结构标题 title	Structure of a cytochrome c peroxidase-cytochrome c site specific cross-link
关键词 keywords	OXIDOREDUCTASE, heme enzyme, electron transfer, OXIDOREDUCTASE-ELECTRON TRANSPORT COMPLEX; OXIDOREDUCTASE/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	30.71 Å
回转半径 Rg (电子) rg_electron	29.81 Å
零角强度 I(0) i0	139309000.00
分子量 molecular_weight	93703.0 kDa
排除体积 excluded_volume	116930 Å³
包络体积 envelope_volume	140650 Å³
水化壳体积 shell_volume	39217 Å³
包络直径 envelope_diameter	100.9 Å
壳层 Rg shell_rg	37.09 Å
包络 Rg envelope_rg	29.80 Å
形状 Rg shape_rg	29.81 Å
总 Rg total_rg	30.44 Å
总原子数 total_atoms	6611
残基数 n_residues	804
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	99.1 Å
Rg (实空间) rg_real	30.66 Å
Rg 误差 (实空间) rg_real_error	0.50 Å
I(0) (实空间) i0_real	1.3930e+08
I(0) 误差 (实空间) i0_real_error	1.7390e+06
Rg (倒空间) rg_reciprocal	30.69 Å
I(0) (倒空间) i0_reciprocal	139300000.0000
解质量估计 total_estimate	0.8999
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	0.281
峰度 Kurtosis kurtosis	-0.459
角度范围 angular_range	— – 0.2600 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	32620000.0000
实空间数据点数 n_real_points	53
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.919; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.943

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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 c peroxidase, mitochondrial
分子量 formula_weight	33543.2 kDa
EC 编号 ec_number	1.11.1.5
突变 mutation	C128A, V197C
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,C
原子数 atom_count	7343

TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHTSGTWDKHDNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQGPKIPWRAGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKTHLKNSGYEGPWGAANNCFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQDPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;baker's yeast ;
NCBI 分类编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

描述 description	Cytochrome c, iso-1
分子量 formula_weight	12073.8 kDa
突变 mutation	A81C, C102T
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	B,D

AEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKKNVLWDENNMSEYLTNPKKYIPGTKMCFGGLKKEKDRNDLITYLKKATE

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;baker's yeast ;
NCBI 分类编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 3 non-polymer

描述 description	IODIDE ION
分子量 formula_weight	126.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 4 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 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	732

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6. 折叠分类 (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1s6va_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.93 — Heme-dependent peroxidases
超家族 Superfamily superfamily	a.93.1 — Heme-dependent peroxidases
家族 Family family	a.93.1.1 — CCP-like

结构域编号 domain_id	d1s6vb_
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	d1s6vc_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.93 — Heme-dependent peroxidases
超家族 Superfamily superfamily	a.93.1 — Heme-dependent peroxidases
家族 Family family	a.93.1.1 — CCP-like

结构域编号 domain_id	d1s6vd_
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 (6 domains)

结构域编号 domain_id	1s6vA01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	520 — Peroxidase; domain 1
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1s6vA02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	420 — Peroxidase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Peroxidase, domain 2

结构域编号 domain_id	1s6vB00
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	1s6vC01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	520 — Peroxidase; domain 1
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1s6vC02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	420 — Peroxidase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Peroxidase, domain 2

结构域编号 domain_id	1s6vD00
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 (2)

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晶胞边长 a length_a	45.240 Å
晶胞边长 b length_b	107.920 Å
晶胞边长 c length_c	88.380 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	104.42 °
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	1.880 Å
最低分辨率 resolution_low	45.650 Å
R 因子 r_factor	0.1900
R_work r_work	0.1900
R_free r_free	0.2430

fit	/app/data/saxs_computation/s6/1s6v/1s6v.fit
pddf	/app/data/pr_computation/s6/1s6v/1s6v.pr.out
profile	/app/data/saxs_computation/s6/1s6v/1s6v.dat

Structure of a cytochrome c peroxidase-cytochrome c site specific cross-link

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

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 water

6. 折叠分类 (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

CATH v4.4 (6 domains)

7. 引用文献 (2)

8. 文件与曲线 (10)

Files (7)

Curves (3)