8hkj

Crystal structure of the CYP102A5 haem Domain isolated from Bacillus cereus

Method: X-RAY DIFFRACTION D_max: 232.8 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

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8hkj
沉积日期 deposition_date	2022-11-27
结构标题 title	Crystal structure of the CYP102A5 haem Domain isolated from Bacillus cereus
关键词 keywords	Cytochrome P450, Monooxygenase, 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	64.62 Å
回转半径 Rg (电子) rg_electron	64.83 Å
零角强度 I(0) i0	4413650000.00
分子量 molecular_weight	582870.0 kDa
排除体积 excluded_volume	737530 Å³
包络体积 envelope_volume	1037200 Å³
水化壳体积 shell_volume	133120 Å³
包络直径 envelope_diameter	214.2 Å
壳层 Rg shell_rg	65.05 Å
包络 Rg envelope_rg	63.30 Å
形状 Rg shape_rg	64.83 Å
总 Rg total_rg	64.85 Å
总原子数 total_atoms	41062
残基数 n_residues	4996
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	232.8 Å
Rg (实空间) rg_real	65.57 Å
Rg 误差 (实空间) rg_real_error	1.73 Å
I(0) (实空间) i0_real	4.4200e+09
I(0) 误差 (实空间) i0_real_error	9.2160e+07
Rg (倒空间) rg_reciprocal	64.25 Å
I(0) (倒空间) i0_reciprocal	4408000000.0000
解质量估计 total_estimate	0.8073
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	223.1 Å
偏度 Skewness skewness	0.481
峰度 Kurtosis kurtosis	-0.419
角度范围 angular_range	— – 0.1200 Å⁻¹
当前正则化参数 α current_alpha	0.1632
最高正则化参数 α highest_alpha	1946000000.0000
实空间数据点数 n_real_points	25
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.557; Stabil: 0.996; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.825

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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	Bifunctional cytochrome P450/NADPH--P450 reductase
分子量 formula_weight	52925.6 kDa
来源方法 src_method	man
拷贝数 entity_count	12

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F,G,H,I,J,K,L
原子数 atom_count	41062

MEKKVSAIPQPKTYGPLGNLPLIDKDKPTLSFIKIAEEYGPIFQIQTLSDTIIVVSGHELVAEVCDETRFDKSIEGALAKVRAFAGDGLFTSETHEPNWKKAHNILMPTFSQRAMKDYHAMMVDIAVQLVQKWARLNPNENVDVPEDMTRLTLDTIGLCGFNYRFNSFYRETPHPFITSMTRALDEAMHQLQRLDIEDKLMWRTKRQFQHDIQSMFSLVDNIIAERKSSGDQEENDLLSRMLNVPDPETGEKLDDENIRFQIITFLIAGHETTSGLLSFAIYFLLKNPDKLKKAYEEVDRVLTDPTPTYQQVMKLKYMRMILNESLRLWPTAPAFSLYAKEDTVIGGKYPIKKGEDRISVLIPQLHRDKDAWGDNVEEFQPERFEELDKVPHHAYKPFGNGQRACIGMQFALHEATLVMGMLLQHFELIDYQNYQLDVKQTLTLKPGDFKIRILPRKQ

来源 Source

来源生物 organism	Bacillus cereus
NCBI 分类编号 ncbi_taxonomy_id	1396
宿主生物 host_organism	Escherichia coli

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	12

Entity 3 non-polymer

描述 description	PALMITIC ACID
分子量 formula_weight	256.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	12

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7. 引用文献 (1)

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晶胞边长 a length_a	96.620 Å
晶胞边长 b length_b	126.060 Å
晶胞边长 c length_c	141.440 Å
晶胞夹角 α angle_alpha	86.66 °
晶胞夹角 β angle_beta	79.47 °
晶胞夹角 γ angle_gamma	84.97 °
晶胞分子数 Z z_pdb	12

空间群 space_group	P 1
空间群编号 int_tables_number	1
晶系 crystal_system	—

分辨率 resolution	2.800 Å
最低分辨率 resolution_low	19.960 Å
R 因子 r_factor	0.2404
R_work r_work	0.2388
R_free r_free	0.2696

fit	/app/data/saxs_computation/hk/8hkj/8hkj.fit
pddf	/app/data/pr_computation/hk/8hkj/8hkj.pr.out
profile	/app/data/saxs_computation/hk/8hkj/8hkj.dat

Crystal structure of the CYP102A5 haem Domain isolated from Bacillus cereus

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