8jua

Multifunctional cytochrome P450 enzyme IkaD from Streptomyces sp. ZJ306, in complex with epoxyikarugamycin

Method: X-RAY DIFFRACTION D_max: 85.8 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

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8jua
沉积日期 deposition_date	2023-06-26
结构标题 title	Multifunctional cytochrome P450 enzyme IkaD from Streptomyces sp. ZJ306, in complex with epoxyikarugamycin
关键词 keywords	;C-H functionalization, regioselectivity, chemoselectivity, polycyclic tetramate macrolactam (PoTeM), cytochrome P450 enzyme, OXIDOREDUCTASE ;; OXIDOREDUCTASE
实验方法 method	X-RAY DIFFRACTION

▼

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	28.11 Å
回转半径 Rg (电子) rg_electron	26.85 Å
零角强度 I(0) i0	127039000.00
分子量 molecular_weight	89099.0 kDa
排除体积 excluded_volume	111530 Å³
包络体积 envelope_volume	131410 Å³
水化壳体积 shell_volume	39434 Å³
包络直径 envelope_diameter	91.1 Å
壳层 Rg shell_rg	35.36 Å
包络 Rg envelope_rg	26.80 Å
形状 Rg shape_rg	26.85 Å
总 Rg total_rg	27.66 Å
总原子数 total_atoms	12389
残基数 n_residues	780
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

▼

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	85.8 Å
Rg (实空间) rg_real	27.93 Å
Rg 误差 (实空间) rg_real_error	0.44 Å
I(0) (实空间) i0_real	1.2700e+08
I(0) 误差 (实空间) i0_real_error	1.4480e+06
Rg (倒空间) rg_reciprocal	27.99 Å
I(0) (倒空间) i0_reciprocal	127000000.0000
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	2
主峰位置 r_peak_primary	35.2 Å
偏度 Skewness skewness	0.194
峰度 Kurtosis kurtosis	-0.433
角度范围 angular_range	— – 0.2800 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	38960000.0000
实空间数据点数 n_real_points	57
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.929; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.937

▶

4. 晶体学与实验 4. Crystallography & Experiment

▶

5. 实体与聚合体信息 (5)

Entity 1 polymer

描述 description	Cytochrome P450
分子量 formula_weight	48058.5 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	13148

MGSSHHHHHHSSGLVPRGSHMPGQQEQQAPSEHPEQQELLTFPFASTGLEFPPVYHELYQQRLTKVRLPYGDDAYLAIRYADVKTVLSDSRFSIVASLGQDQPRTRAGARVGNGLFSLDPPQHSRLRSVLGRDFTPRRVEKLRERVRELTDQCLDRMEAAGSPADLVAHLAVPMPTAVVCEMMGVPEPDHHLFWGWAETILSNDTTPDDLIRRYQEFTAYMGAMVEERRARPTDDMFGMLVRACDEEGRITEIEMHALASDLLSAGFVSTAHQIANFTAMLLARPERLQPLVDKPEQIPAAVEELMRHVPILSGFSFPRYATEDLEMSGVTVRRGEAVIPVIAAANRDPDVYPDAGRLDLERNGLPHLGFGQGPHFCIGAHLARVELQVVLEALTERFPDLRFGIPENALKWKRGHFMNGLHELPVAW

来源 Source

来源生物 organism	Streptomyces sp. ZJ306
NCBI 分类编号 ncbi_taxonomy_id	1469403
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 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	2

Entity 3 non-polymer

描述 description	;(1Z,3E,5S,7R,8R,10R,11R,12S,13R,15S,16R,17S,19Z,26S)-11-ethyl-2-hydroxy-10-methyl-22,27-diaza-14 oxahexacyclo[24.2.1.05,17.07,16.013,15.08,12]nonacosa-1(2),3,19-triene-21,28,29-trione ;
分子量 formula_weight	494.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 non-polymer

描述 description	FORMIC ACID
分子量 formula_weight	46.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	8

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	747

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	92.620 Å
晶胞边长 b length_b	81.939 Å
晶胞边长 c length_c	144.165 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	94.39 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

空间群 space_group	I 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	monoclinic

分辨率 resolution	2.000 Å
最低分辨率 resolution_low	23.310 Å
R 因子 r_factor	0.2065
R_work r_work	0.2038
R_free r_free	0.2557

fit	/app/data/saxs_computation/ju/8jua/8jua.fit
pddf	/app/data/pr_computation/ju/8jua/8jua.pr.out
profile	/app/data/saxs_computation/ju/8jua/8jua.dat

Multifunctional cytochrome P450 enzyme IkaD from Streptomyces sp. ZJ306, in complex with epoxyikarugamycin

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