9kgp

The structure of natural P450BM3-H derived from Bacillus megaterium for catalyzing the steroid DHEA

Method: X-RAY DIFFRACTION D_max: 101.5 Å Quality: GOOD

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	9kgp
沉积日期 deposition_date	2024-11-08
结构标题 title	The structure of natural P450BM3-H derived from Bacillus megaterium for catalyzing the steroid DHEA
关键词 keywords	Oxidoreductase, cytochrome P450BM3, heme-binding domain, steroid compound, dehydroepiandrosterone DHEA; 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	31.95 Å
回转半径 Rg (电子) rg_electron	30.91 Å
零角强度 I(0) i0	167215000.00
分子量 molecular_weight	104680.0 kDa
排除体积 excluded_volume	131580 Å³
包络体积 envelope_volume	161980 Å³
水化壳体积 shell_volume	42866 Å³
包络直径 envelope_diameter	108.0 Å
壳层 Rg shell_rg	38.72 Å
包络 Rg envelope_rg	30.95 Å
形状 Rg shape_rg	30.92 Å
总 Rg total_rg	31.52 Å
总原子数 total_atoms	7376
残基数 n_residues	906
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	101.5 Å
Rg (实空间) rg_real	31.90 Å
Rg 误差 (实空间) rg_real_error	0.73 Å
I(0) (实空间) i0_real	1.6720e+08
I(0) 误差 (实空间) i0_real_error	2.6810e+06
Rg (倒空间) rg_reciprocal	31.92 Å
I(0) (倒空间) i0_reciprocal	167200000.0000
解质量估计 total_estimate	0.8958
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	36.6 Å
偏度 Skewness skewness	0.303
峰度 Kurtosis kurtosis	-0.432
角度范围 angular_range	— – 0.2500 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	41420000.0000
实空间数据点数 n_real_points	51
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.913; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.902

▶

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

▶

5. 实体与聚合体信息 (3)

Entity 1 polymer

描述 description	Bifunctional cytochrome P450/NADPH--P450 reductase
分子量 formula_weight	52078.3 kDa
EC 编号 ec_number	1.14.14.1,1.6.2.4
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	7928

TIKEMPQPKTFGELKNLPLLNTDKPVQALMKIADELGEIFKFEAPGRVTRYLSSQRLIKEACDESRFDKNLSQGLKFVRDFAGDGLVTSWTHEKNWKKAHNILLPSFSQQAMKGYHAMMVDIAVQLIQKWERLNADEHIEVPEDMTRLTLDTIGLCGFNYRFNSFYRDQPHPFITSMVRALDEIMNKLQRANPDDPAYDENKRQFQDDIKVMNDLVDKIIADRKASGEQSDDLLTHMLNGKDPETGEPLDDENIRYQIITFLGGGHETTSGLLSFALYFLVKNPHVLQKAAEEAARILVDPVPSYKQVKQLKYVGMVLNEALRLWPTGPAFSLYAKEDTVLGGEYPLEKGDELMVLIPQLHRDKTIWGDDVEEFRPERFENPSAIPQHAFKPFGNGQRACIGQQFALHEATLVLGMMLKHFDFEDHTNYELDIKETLTLKPEGFVVKAKSKQIPL

来源 Source

来源生物 organism	Priestia megaterium NBRC 15308 = ATCC 14581
通用名 common_name	Bacillus megaterium
NCBI 分类编号 ncbi_taxonomy_id	1348623
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 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	552

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	58.914 Å
晶胞边长 b length_b	145.713 Å
晶胞边长 c length_c	63.233 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	97.51 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

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	1.520 Å
最低分辨率 resolution_low	72.820 Å
R 因子 r_factor	0.2250
R_work r_work	0.2210
R_free r_free	0.2270

fit	/app/data/saxs_computation/kg/9kgp/9kgp.fit
pddf	/app/data/pr_computation/kg/9kgp/9kgp.pr.out
profile	/app/data/saxs_computation/kg/9kgp/9kgp.dat

The structure of natural P450BM3-H derived from Bacillus megaterium for catalyzing the steroid DHEA

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