SAXSdb — 1icc

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1icc
沉积日期 deposition_date	2001-03-30
结构标题 title	RAT OUTER MITOCHONDRIAL MEMBRANE CYTOCHROME B5
关键词 keywords	CYTOCHROME, HEME, 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	24.21 Å
回转半径 Rg (电子) rg_electron	23.42 Å
零角强度 I(0) i0	31818000.00
分子量 molecular_weight	41999.0 kDa
排除体积 excluded_volume	51823 Å³
包络体积 envelope_volume	64985 Å³
水化壳体积 shell_volume	23462 Å³
包络直径 envelope_diameter	78.2 Å
壳层 Rg shell_rg	29.91 Å
包络 Rg envelope_rg	23.39 Å
形状 Rg shape_rg	23.41 Å
总 Rg total_rg	24.22 Å
总原子数 total_atoms	2962
残基数 n_residues	344
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	76.2 Å
Rg (实空间) rg_real	24.18 Å
Rg 误差 (实空间) rg_real_error	0.36 Å
I(0) (实空间) i0_real	3.1820e+07
I(0) 误差 (实空间) i0_real_error	4.3370e+05
Rg (倒空间) rg_reciprocal	24.19 Å
I(0) (倒空间) i0_reciprocal	31820000.0000
解质量估计 total_estimate	0.9090
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	28.6 Å
偏度 Skewness skewness	0.276
峰度 Kurtosis kurtosis	-0.488
角度范围 angular_range	— – 0.3300 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	9494000.0000
实空间数据点数 n_real_points	65
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.946; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.982

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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 (4)

Entity 1 polymer

描述 description	CYTOCHROME B5 OUTER MITOCHONDRIAL MEMBRANE ISOFORM
分子量 formula_weight	10007.0 kDa
突变 mutation	A18S, I32L, L47R
来源方法 src_method	man
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	3210

DPAVTYYRLEEVAKRNTSEETWMVIHGRVYDLTRFLSEHPGGEEVLREQAGADATESFEDVGHSPDAREMLKQYYIGDVHPNDLKPK

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	Norway rat
NCBI 分类编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Escherichia coli BL21

Entity 2 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 3 non-polymer

描述 description	PROTOPORPHYRIN IX CONTAINING FE
分子量 formula_weight	616.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 4 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	248

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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	d1icca_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.120 — Cytochrome b5-like heme/steroid binding domain
超家族 Superfamily superfamily	d.120.1 — Cytochrome b5-like heme/steroid binding domain
家族 Family family	d.120.1.1 — Cytochrome b5

结构域编号 domain_id	d1iccb_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.120 — Cytochrome b5-like heme/steroid binding domain
超家族 Superfamily superfamily	d.120.1 — Cytochrome b5-like heme/steroid binding domain
家族 Family family	d.120.1.1 — Cytochrome b5

结构域编号 domain_id	d1iccc_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.120 — Cytochrome b5-like heme/steroid binding domain
超家族 Superfamily superfamily	d.120.1 — Cytochrome b5-like heme/steroid binding domain
家族 Family family	d.120.1.1 — Cytochrome b5

结构域编号 domain_id	d1iccd_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.120 — Cytochrome b5-like heme/steroid binding domain
超家族 Superfamily superfamily	d.120.1 — Cytochrome b5-like heme/steroid binding domain
家族 Family family	d.120.1.1 — Cytochrome b5

CATH v4.4 (4 domains)

结构域编号 domain_id	1iccA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	120 — Flavocytochrome B2; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Cytochrome b5-like heme/steroid binding domain

结构域编号 domain_id	1iccB00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	120 — Flavocytochrome B2; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Cytochrome b5-like heme/steroid binding domain

结构域编号 domain_id	1iccC00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	120 — Flavocytochrome B2; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Cytochrome b5-like heme/steroid binding domain

结构域编号 domain_id	1iccD00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	120 — Flavocytochrome B2; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Cytochrome b5-like heme/steroid binding domain

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7. 引用文献 (1)

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晶胞边长 a length_a	39.904 Å
晶胞边长 b length_b	51.315 Å
晶胞边长 c length_c	167.419 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	16

空间群 space_group	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	2.000 Å
最低分辨率 resolution_low	50.000 Å
R 因子 r_factor	0.2200
R_work r_work	0.1960
R_free r_free	0.2400

fit	/app/data/saxs_computation/ic/1icc/1icc.fit
pddf	/app/data/pr_computation/ic/1icc/1icc.pr.out
profile	/app/data/saxs_computation/ic/1icc/1icc.dat

RAT OUTER MITOCHONDRIAL MEMBRANE CYTOCHROME B5

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 (4)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 non-polymer

Entity 3 non-polymer

Entity 4 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 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)