SAXSdb — 2bpo

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2bpo
沉积日期 deposition_date	2005-04-21
结构标题 title	Crystal structure of the yeast CPR triple mutant: D74G, Y75F, K78A.
关键词 keywords	REDUCTASE, NADPH-CYTOCHROME P450 REDUCTASE, CPR, DIFLAVIN REDUCTASE, FAD, FMN-BINDING, NADP, ELECTRON TRANSFER; REDUCTASE
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	41.95 Å
回转半径 Rg (电子) rg_electron	42.23 Å
零角强度 I(0) i0	327099000.00
分子量 molecular_weight	146800.0 kDa
排除体积 excluded_volume	183050 Å³
包络体积 envelope_volume	237710 Å³
水化壳体积 shell_volume	49982 Å³
包络直径 envelope_diameter	145.1 Å
壳层 Rg shell_rg	43.43 Å
包络 Rg envelope_rg	42.11 Å
形状 Rg shape_rg	42.21 Å
总 Rg total_rg	42.34 Å
总原子数 total_atoms	10343
残基数 n_residues	1282
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	137.3 Å
Rg (实空间) rg_real	42.36 Å
Rg 误差 (实空间) rg_real_error	1.31 Å
I(0) (实空间) i0_real	3.2710e+08
I(0) 误差 (实空间) i0_real_error	6.0810e+06
Rg (倒空间) rg_reciprocal	41.96 Å
I(0) (倒空间) i0_reciprocal	327000000.0000
解质量估计 total_estimate	0.5611
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	36.1 Å
偏度 Skewness skewness	0.575
峰度 Kurtosis kurtosis	-0.393
角度范围 angular_range	— – 0.1900 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	66380000.0000
实空间数据点数 n_real_points	39
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.724; Stabil: 1.000; Sysdev: 0.008; Positv: 1.000; Valcen: 0.887; Smooth: 0.207

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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 (6)

Entity 1 polymer

描述 description	NADPH-CYTOCHROM P450 REDUCTASE
分子量 formula_weight	75710.9 kDa
EC 编号 ec_number	1.6.2.4
突变 mutation	YES
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	10528

MGSSHHHHHHSSGLVPRGSHMLDIMSDDGDITAVSSGNRDIAQVVTENNKNYLVLYASQTGTAEGFAKAFSKELVAKFNLNVMCADVENYDFESLNDVPVIVSIFISTYGEGDFPDGAVNFEDFICNAEAGALSNLRYNMFGLGNSTYEFFNGAAKKAEKHLSAAGAIRLGKLGEADDGAGTTDEDYMAWKDSILEVLKDELHLDEQEAKFTSQFQYTVLNEITDSMSLGEPSAHYLPSHQLNRNADGIQLGPFDLSQPYIAPIVKSRELFSSNDRNCIHSEFDLSGSNIKYSTGDHLAVWPSNPLEKVEQFLSIFNLDPETIFDLKPLDPTVKVPFPTPTTIGAAIKHYLEITGPVSRQLFSSLIQFAPNADVKEKLTLLSKDKDQFAVEITSKYFNIADALKYLSDGAKWDTVPMQFLVESVPQMTPRYYSISSSSLSEKQTVHVTSIVENFPNPELPDAPPVVGVTTNLLRNIQLAQNNVNIAETNLPVHYDLNGPRKLFANYKLPVHVRRSNFRLPSNPSTPVIMIGPGTGVAPFRGFIRERVAFLESQKKGGNNVSLGKHILFYGSRNTDDFLYQDEWPEYAKKLDGSFEMVVAHSRLPNTKKVYVQDKLKDYEDQVFEMINNGAFIYVCGDAKGMAKGVSTALVGILSRGKSITTDEATELIKMLKTSGRYQEDVW

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 non-polymer

描述 description	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 6 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	185

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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	2bpoA01
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	2bpoA02
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	2bpoA03
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	2bpoA04
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	2bpoB01
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	2bpoB02
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	2bpoB03
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	2bpoB04
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	78.357 Å
晶胞边长 b length_b	86.596 Å
晶胞边长 c length_c	259.717 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	2.900 Å
最低分辨率 resolution_low	39.180 Å
R 因子 r_factor	0.2050
R_work r_work	0.2050
R_free r_free	0.2680

fit	/app/data/saxs_computation/bp/2bpo/2bpo.fit
pddf	/app/data/pr_computation/bp/2bpo/2bpo.pr.out
profile	/app/data/saxs_computation/bp/2bpo/2bpo.dat

Crystal structure of the yeast CPR triple mutant: D74G, Y75F, K78A.

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