2bgj

X-Ray Structure of the Ferredoxin-NADP(H) Reductase from Rhodobacter capsulatus at 2.1 Angstroms

Method: X-RAY DIFFRACTION D_max: 102.0 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	2bgj
沉积日期 deposition_date	2004-12-23
结构标题 title	X-Ray Structure of the Ferredoxin-NADP(H) Reductase from Rhodobacter capsulatus at 2.1 Angstroms
关键词 keywords	FERREDOXIN(FLAVODOXIN)-NADP(H) REDUCTASE, FLAVOPROTEINS, ELECTRON TRANSFER, RHODOBACTER CAPSULATUS, OXIDOREDUCTASE; OXIDOREDUCTASE
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	33.19 Å
回转半径 Rg (电子) rg_electron	32.14 Å
零角强度 I(0) i0	220164000.00
分子量 molecular_weight	118910.0 kDa
排除体积 excluded_volume	148910 Å³
包络体积 envelope_volume	186750 Å³
水化壳体积 shell_volume	47474 Å³
包络直径 envelope_diameter	104.9 Å
壳层 Rg shell_rg	40.12 Å
包络 Rg envelope_rg	31.34 Å
形状 Rg shape_rg	32.09 Å
总 Rg total_rg	32.94 Å
总原子数 total_atoms	8360
残基数 n_residues	1031
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	102.0 Å
Rg (实空间) rg_real	32.94 Å
Rg 误差 (实空间) rg_real_error	0.68 Å
I(0) (实空间) i0_real	2.2020e+08
I(0) 误差 (实空间) i0_real_error	3.6140e+06
Rg (倒空间) rg_reciprocal	33.05 Å
I(0) (倒空间) i0_reciprocal	220200000.0000
解质量估计 total_estimate	0.9012
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	46.7 Å
偏度 Skewness skewness	0.062
峰度 Kurtosis kurtosis	-0.564
角度范围 angular_range	— – 0.2400 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	60920000.0000
实空间数据点数 n_real_points	49
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.933; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.923

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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 (3)

Entity 1 polymer

描述 description	FERREDOXIN-NADP(H) REDUCTASE
分子量 formula_weight	30436.9 kDa
EC 编号 ec_number	1.18.1.2
突变 mutation	YES
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	8711

TTVNETTPIAPAKVLPDAQTVTSVRHWTDTLFSFRVTRPQTLRFRSGEFVMIGLLDDNGKPIMRAYSIASPAWDEELEFYSIKVPDGPLTSRLQHIKVGEQIILRPKPVGTLVIDALLPGKRLWFLATGTGIAPFASLMREPEAYEKFDEVIMMHACRTVAELEYGRQLVEALQEDPLIGELVEGKLKYYPTTTREEFHHMGRITDNLASGKVFEDLGIAPMNPETDRAMVCGSLAFNVDVMKVLESYGLREGANSEPREFVVEKAFVGEGI

来源 Source

来源生物 organism	RHODOBACTER CAPSULATUS
NCBI 分类编号 ncbi_taxonomy_id	1061
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 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	4

Entity 3 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	351

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6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d2bgja1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.43 — Reductase/isomerase/elongation factor common domain
超家族 Superfamily superfamily	b.43.4 — Riboflavin synthase domain-like
家族 Family family	b.43.4.0 — automated matches

结构域编号 domain_id	d2bgja2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.25 — Ferredoxin reductase-like, C-terminal NADP-linked domain
超家族 Superfamily superfamily	c.25.1 — Ferredoxin reductase-like, C-terminal NADP-linked domain
家族 Family family	c.25.1.0 — automated matches

结构域编号 domain_id	d2bgjb1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.43 — Reductase/isomerase/elongation factor common domain
超家族 Superfamily superfamily	b.43.4 — Riboflavin synthase domain-like
家族 Family family	b.43.4.0 — automated matches

结构域编号 domain_id	d2bgjb2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.25 — Ferredoxin reductase-like, C-terminal NADP-linked domain
超家族 Superfamily superfamily	c.25.1 — Ferredoxin reductase-like, C-terminal NADP-linked domain
家族 Family family	c.25.1.0 — automated matches

结构域编号 domain_id	d2bgjc1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.43 — Reductase/isomerase/elongation factor common domain
超家族 Superfamily superfamily	b.43.4 — Riboflavin synthase domain-like
家族 Family family	b.43.4.0 — automated matches

结构域编号 domain_id	d2bgjc2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.25 — Ferredoxin reductase-like, C-terminal NADP-linked domain
超家族 Superfamily superfamily	c.25.1 — Ferredoxin reductase-like, C-terminal NADP-linked domain
家族 Family family	c.25.1.0 — automated matches

结构域编号 domain_id	d2bgjd1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.43 — Reductase/isomerase/elongation factor common domain
超家族 Superfamily superfamily	b.43.4 — Riboflavin synthase domain-like
家族 Family family	b.43.4.0 — automated matches

结构域编号 domain_id	d2bgjd2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.25 — Ferredoxin reductase-like, C-terminal NADP-linked domain
超家族 Superfamily superfamily	c.25.1 — Ferredoxin reductase-like, C-terminal NADP-linked domain
家族 Family family	c.25.1.0 — automated matches

CATH v4.4 (8 domains)

结构域编号 domain_id	2bgjA01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
同源超家族 H-superfamily homologous superfamily	10 — Translation factors

结构域编号 domain_id	2bgjA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	80 — Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module

结构域编号 domain_id	2bgjB01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
同源超家族 H-superfamily homologous superfamily	10 — Translation factors

结构域编号 domain_id	2bgjB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	80 — Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module

结构域编号 domain_id	2bgjC01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
同源超家族 H-superfamily homologous superfamily	10 — Translation factors

结构域编号 domain_id	2bgjC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	80 — Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module

结构域编号 domain_id	2bgjD01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
同源超家族 H-superfamily homologous superfamily	10 — Translation factors

结构域编号 domain_id	2bgjD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	80 — Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module

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7. 引用文献 (3)

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晶胞边长 a length_a	69.290 Å
晶胞边长 b length_b	93.626 Å
晶胞边长 c length_c	103.427 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.08 °
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	2.100 Å
最低分辨率 resolution_low	105.410 Å
R 因子 r_factor	0.2155
R_work r_work	0.2155
R_free r_free	0.2432

fit	/app/data/saxs_computation/bg/2bgj/2bgj.fit
pddf	/app/data/pr_computation/bg/2bgj/2bgj.pr.out
profile	/app/data/saxs_computation/bg/2bgj/2bgj.dat