1fcd

;THE STRUCTURE OF FLAVOCYTOCHROME C SULFIDE DEHYDROGENASE FROM A PURPLE PHOTOTROPHIC BACTERIUM CHROMATIUM VINOSUM AT 2.5 ANGSTROMS RESOLUTION ;

Method: X-RAY DIFFRACTION D_max: 108.7 Å Quality: EXCELLENT

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	1fcd
沉积日期 deposition_date	1994-08-18
结构标题 title	;THE STRUCTURE OF FLAVOCYTOCHROME C SULFIDE DEHYDROGENASE FROM A PURPLE PHOTOTROPHIC BACTERIUM CHROMATIUM VINOSUM AT 2.5 ANGSTROMS RESOLUTION ;
关键词 keywords	ELECTRON TRANSPORT(FLAVOCYTOCHROME); ELECTRON TRANSPORT(FLAVOCYTOCHROME)
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	34.69 Å
回转半径 Rg (电子) rg_electron	34.06 Å
零角强度 I(0) i0	256444000.00
分子量 molecular_weight	128020.0 kDa
排除体积 excluded_volume	159470 Å³
包络体积 envelope_volume	195860 Å³
水化壳体积 shell_volume	47128 Å³
包络直径 envelope_diameter	116.8 Å
壳层 Rg shell_rg	41.33 Å
包络 Rg envelope_rg	33.75 Å
形状 Rg shape_rg	34.03 Å
总 Rg total_rg	34.66 Å
总原子数 total_atoms	9002
残基数 n_residues	1150
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	108.7 Å
Rg (实空间) rg_real	34.60 Å
Rg 误差 (实空间) rg_real_error	0.70 Å
I(0) (实空间) i0_real	2.5640e+08
I(0) 误差 (实空间) i0_real_error	3.9300e+06
Rg (倒空间) rg_reciprocal	34.66 Å
I(0) (倒空间) i0_reciprocal	256500000.0000
解质量估计 total_estimate	0.9020
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	44.9 Å
偏度 Skewness skewness	0.193
峰度 Kurtosis kurtosis	-0.556
角度范围 angular_range	— – 0.2300 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	127200000.0000
实空间数据点数 n_real_points	47
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.953; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.863

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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	FLAVOCYTOCHROME C SULFIDE DEHYDROGENASE (FLAVIN-BINDING SUBUNIT)
分子量 formula_weight	42844.2 kDa
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,B
原子数 atom_count	9002

AGRKVVVVGGGTGGATAAKYIKLADPSIEVTLIEPNTDYYTCYLSNEVIGGDRKLESIKHGYDGLRAHGIQVVHDSATGIDPDKKLVKTAGGAEFGYDRCVVAPGIELIYDKIEGYSEEAAAKLPHAWKAGEQTAILRKQLEDMADGGTVVIAPPAAPFRCPPGPYERASQVAYYLKAHKPMSKVIILDSSQTFSKQSQFSKGWERLYGFGTENAMIEWHPGPDSAVVKVDGGEMMVETAFGDEFKADVINLIPPQRAGKIAQIAGLTNDAGWCPVDIKTFESSIHKGIHVIGDASIANPMPKSGYSANSQGKVAAAAVVVLLKGEEPGTPSYLNTCYSILAPAYGISVAAIYRPNADGSAIESVPDSGGVTPVDAPDWVLEREVQYAYSWYNNIVHDTFG

来源 Source

来源生物 organism	Allochromatium vinosum
NCBI 分类编号 ncbi_taxonomy_id	1049

Entity 2 polymer

描述 description	FLAVOCYTOCHROME C SULFIDE DEHYDROGENASE (CYTOCHROME SUBUNIT)
分子量 formula_weight	19231.7 kDa
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	C,D

EPTAEMLTNNCAGCHGTHGNSVGPASPSIAQMDPMVFVEVMEGFKSGEIASTIMGRIAKGYSTADFEKMAGYFKQQTYQPAKQSFDTALADTGAKLHDKYCEKCHVEGGKPLADEEDYHILAGQWTPYLQYAMSDFREERRPMEKKMASKLRELLKAEGDAGLDALFAFYASQQ

来源 Source

来源生物 organism	Allochromatium vinosum
NCBI 分类编号 ncbi_taxonomy_id	1049

Entity 3 non-polymer

描述 description	FLAVIN-ADENINE DINUCLEOTIDE
分子量 formula_weight	785.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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

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6. 折叠分类 (SCOP + CATH) 20 domains

SCOP 2.08 (10 domains)

结构域编号 domain_id	d1fcda1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.3 — FAD/NAD(P)-binding domain
超家族 Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
家族 Family family	c.3.1.5 — FAD/NAD-linked reductases, N-terminal and central domains

结构域编号 domain_id	d1fcda2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.3 — FAD/NAD(P)-binding domain
超家族 Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
家族 Family family	c.3.1.5 — FAD/NAD-linked reductases, N-terminal and central domains

结构域编号 domain_id	d1fcda3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.87 — CO dehydrogenase flavoprotein C-domain-like
超家族 Superfamily superfamily	d.87.1 — FAD/NAD-linked reductases, dimerisation (C-terminal) domain
家族 Family family	d.87.1.1 — FAD/NAD-linked reductases, dimerisation (C-terminal) domain

结构域编号 domain_id	d1fcdb1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.3 — FAD/NAD(P)-binding domain
超家族 Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
家族 Family family	c.3.1.5 — FAD/NAD-linked reductases, N-terminal and central domains

结构域编号 domain_id	d1fcdb2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.3 — FAD/NAD(P)-binding domain
超家族 Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
家族 Family family	c.3.1.5 — FAD/NAD-linked reductases, N-terminal and central domains

结构域编号 domain_id	d1fcdb3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.87 — CO dehydrogenase flavoprotein C-domain-like
超家族 Superfamily superfamily	d.87.1 — FAD/NAD-linked reductases, dimerisation (C-terminal) domain
家族 Family family	d.87.1.1 — FAD/NAD-linked reductases, dimerisation (C-terminal) domain

结构域编号 domain_id	d1fcdc1
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.3.1.4 — Two-domain cytochrome c

结构域编号 domain_id	d1fcdc2
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.3.1.4 — Two-domain cytochrome c

结构域编号 domain_id	d1fcdd1
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.3.1.4 — Two-domain cytochrome c

结构域编号 domain_id	d1fcdd2
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.3.1.4 — Two-domain cytochrome c

CATH v4.4 (10 domains)

结构域编号 domain_id	1fcdA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	50 — FAD/NAD(P)-binding domain
同源超家族 H-superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

结构域编号 domain_id	1fcdA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	50 — FAD/NAD(P)-binding domain
同源超家族 H-superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

结构域编号 domain_id	1fcdA03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	760 — Flavocytochrome C Sulfide Dehydrogenase; Chain A Domain 3
同源超家族 H-superfamily homologous superfamily	10 — Flavocytochrome c sulphide dehydrogenase, flavin-binding domain

结构域编号 domain_id	1fcdB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	50 — FAD/NAD(P)-binding domain
同源超家族 H-superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

结构域编号 domain_id	1fcdB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	50 — FAD/NAD(P)-binding domain
同源超家族 H-superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

结构域编号 domain_id	1fcdB03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	760 — Flavocytochrome C Sulfide Dehydrogenase; Chain A Domain 3
同源超家族 H-superfamily homologous superfamily	10 — Flavocytochrome c sulphide dehydrogenase, flavin-binding domain

结构域编号 domain_id	1fcdC01
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	1fcdC02
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	1fcdD01
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	1fcdD02
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 (3)

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晶胞边长 a length_a	168.600 Å
晶胞边长 b length_b	84.600 Å
晶胞边长 c length_c	106.400 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	107.00 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	—

分辨率 resolution	2.530 Å
最低分辨率 resolution_low	— Å
R 因子 r_factor	0.2370
R_work r_work	0.2370
R_free r_free	—

fit	/app/data/saxs_computation/fc/1fcd/1fcd.fit
pddf	/app/data/pr_computation/fc/1fcd/1fcd.pr.out
profile	/app/data/saxs_computation/fc/1fcd/1fcd.dat

;THE STRUCTURE OF FLAVOCYTOCHROME C SULFIDE DEHYDROGENASE FROM A PURPLE PHOTOTROPHIC BACTERIUM CHROMATIUM VINOSUM AT 2.5 ANGSTROMS RESOLUTION ;

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

5. 实体与聚合体信息 (4)

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

6. 折叠分类 (SCOP + CATH) 20 domains

SCOP 2.08 (10 domains)

CATH v4.4 (10 domains)

7. 引用文献 (3)

8. 文件与曲线 (10)

Files (7)

Curves (3)