SAXSdb — 2bn4

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2bn4
沉积日期 deposition_date	2005-03-18
结构标题 title	;A second FMN-binding site in yeast NADPH-cytochrome P450 reductase suggests a novel mechanism of electron transfer by diflavin reductase ;
关键词 keywords	OXIDOREDUCTASE, DIFLAVIN REDUCTASE, CPR, ELECTRON TRANSFER, FMN-BINDING, FAD, FLAVOPROTEIN, NADPH, 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	43.48 Å
回转半径 Rg (电子) rg_electron	43.44 Å
零角强度 I(0) i0	317384000.00
分子量 molecular_weight	145770.0 kDa
排除体积 excluded_volume	181890 Å³
包络体积 envelope_volume	240930 Å³
水化壳体积 shell_volume	48194 Å³
包络直径 envelope_diameter	145.5 Å
壳层 Rg shell_rg	45.68 Å
包络 Rg envelope_rg	42.96 Å
形状 Rg shape_rg	43.43 Å
总 Rg total_rg	43.58 Å
总原子数 total_atoms	10276
残基数 n_residues	1284
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	146.3 Å
Rg (实空间) rg_real	43.81 Å
Rg 误差 (实空间) rg_real_error	1.56 Å
I(0) (实空间) i0_real	3.1740e+08
I(0) 误差 (实空间) i0_real_error	5.8640e+06
Rg (倒空间) rg_reciprocal	43.48 Å
I(0) (倒空间) i0_reciprocal	317300000.0000
解质量估计 total_estimate	0.7298
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	32.5 Å
偏度 Skewness skewness	0.404
峰度 Kurtosis kurtosis	-0.787
角度范围 angular_range	— – 0.1800 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	62690000.0000
实空间数据点数 n_real_points	37
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.606; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.664; Smooth: 0.000

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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	NADPH CYTOCHROME P450 REDUCTASE
分子量 formula_weight	75843.0 kDa
EC 编号 ec_number	1.6.2.4
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	10331

MGSSHHHHHHSSGLVPRGSHMLDIMSDDGDITAVSSGNRDIAQVVTENNKNYLVLYASQTGTAEDYAKKFSKELVAKFNLNVMCADVENYDFESLNDVPVIVSIFISTYGEGDFPDGAVNFEDFICNAEAGALSNLRYNMFGLGNSTYEFFNGAAKKAEKHLSAAGAIRLGKLGEADDGAGTTDEDYMAWKDSILEVLKDELHLDEQEAKFTSQFQYTVLNEITDSMSLGEPSAHYLPSHQLNRNADGIQLGPFDLSQPYIAPIVKSRELFSSNDRNCIHSEFDLSGSNIKYSTGDHLAVWPSNPLEKVEQFLSIFNLDPETIFDLKPLDPTVKVPFPTPTTIGAAIKHYLEITGPVSRQLFSSLIQFAPNADVKEKLTLLSKDKDQFAVEITSKYFNIADALKYLSDGAKWDTVPMQFLVESVPQMTPRYYSISSSSLSEKQTVHVTSIVENFPNPELPDAPPVVGVTTNLLRNIQLAQNNVNIAETNLPVHYDLNGPRKLFANYKLPVHVRRSNFRLPSNPSTPVIMIGPGTGVAPFRGFIRERVAFLESQKKGGNNVSLGKHILFYGSRNTDDFLYQDEWPEYAKKLDGSFEMVVAHSRLPNTKKVYVQDKLKDYEDQVFEMINNGAFIYVCGDAKGMAKGVSTALVGILSRGKSITTDEATELIKMLKTSGRYQEDVW

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

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	2

Entity 3 non-polymer

描述 description	FLAVIN MONONUCLEOTIDE
分子量 formula_weight	456.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 non-polymer

描述 description	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
分子量 formula_weight	743.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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	55

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6. 折叠分类 (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

结构域编号 domain_id	2bn4A01
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	360 — Flavodoxin domain

结构域编号 domain_id	2bn4A02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	990 — NADPH-cytochrome p450 Reductase; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	10 — NADPH-cytochrome p450 Reductase; Chain A, domain 3

结构域编号 domain_id	2bn4A03
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	2bn4A04
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	2bn4B01
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	360 — Flavodoxin domain

结构域编号 domain_id	2bn4B02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	990 — NADPH-cytochrome p450 Reductase; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	10 — NADPH-cytochrome p450 Reductase; Chain A, domain 3

结构域编号 domain_id	2bn4B03
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	2bn4B04
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 (1)

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晶胞边长 a length_a	78.140 Å
晶胞边长 b length_b	77.843 Å
晶胞边长 c length_c	261.495 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	8

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	2.910 Å
最低分辨率 resolution_low	43.410 Å
R 因子 r_factor	0.2330
R_work r_work	0.2330
R_free r_free	0.3000

fit	/app/data/saxs_computation/bn/2bn4/2bn4.fit
pddf	/app/data/pr_computation/bn/2bn4/2bn4.pr.out
profile	/app/data/saxs_computation/bn/2bn4/2bn4.dat

;A second FMN-binding site in yeast NADPH-cytochrome P450 reductase suggests a novel mechanism of electron transfer by diflavin reductase ;

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