9onh

Structure of ancestral-reconstructed cytochrome P450 11A1 (CYP11A1) in complex with desmosterol

Method: X-RAY DIFFRACTION D_max: 78.8 Å Quality: REASONABLE

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	9onh
沉积日期 deposition_date	2025-05-15
最后修订 last_revision	2025-10-22
结构标题 title	Structure of ancestral-reconstructed cytochrome P450 11A1 (CYP11A1) in complex with desmosterol
关键词 keywords	Cytochrome P450, steroidogenesis, evolution, 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	23.85 Å
回转半径 Rg (电子) rg_electron	22.38 Å
零角强度 I(0) i0	44627100.00
分子量 molecular_weight	54367.0 kDa
排除体积 excluded_volume	69184 Å³
包络体积 envelope_volume	79778 Å³
水化壳体积 shell_volume	28824 Å³
包络直径 envelope_diameter	75.4 Å
壳层 Rg shell_rg	30.21 Å
包络 Rg envelope_rg	22.60 Å
形状 Rg shape_rg	22.38 Å
总 Rg total_rg	23.30 Å
总原子数 total_atoms	3885
残基数 n_residues	458
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	78.8 Å
Rg (实空间) rg_real	23.69 Å
Rg 误差 (实空间) rg_real_error	0.48 Å
I(0) (实空间) i0_real	4.4630e+07
I(0) 误差 (实空间) i0_real_error	5.2920e+05
Rg (倒空间) rg_reciprocal	23.73 Å
I(0) (倒空间) i0_reciprocal	44630000.0000
解质量估计 total_estimate	0.6401
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	30.8 Å
偏度 Skewness skewness	0.135
峰度 Kurtosis kurtosis	-0.454
角度范围 angular_range	— – 0.3350 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	9416000.0000
实空间数据点数 n_real_points	65
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.821; Stabil: 0.999; Sysdev: 0.286; Positv: 1.000; Valcen: 0.999; 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 (3)

Entity 1 polymer

描述 description	Ancestral Cytochrome P450 11A1 (CYP11A1)
分子量 formula_weight	56350.8 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	3885

MASGSAVRPFDEIPGNWRNGWLNLYRFWRSNGFRNLHHIMVKNFNKFGPIYREKIGYYESVNIINPEDAATLFKAEGLFPRRLRVEPWVAYRDYRNQKYGVLLKNGEDWRSNRLILNKEVISPNVIQKFVPLLNEVAQDFVSMVHKQIERSGRGKWTVDLSNDLFRFALESVCYVLYGERLGLLQDNPNPESQRFIDSVTLMFKTTSPMLYIPPGLLRRINSKIWRDHVEAWDVIFNHADKCIQKIYRQFRLGQKNENEYPGVLANLLLQGKLPIEDIKASITELMAGGVDTTSMTLLWTLYELARNPHVQEELRAEILAARQQAQGDLSKMLKSVPLLKAAIKETLRLYPVAVSLQRYITEDIVLQNYHIPAGTLVQVGLYAMGRNPEIFPNPEQYNPERWLKREDNHFKSLGFGFGPRQCIGRRIAETEMQLFLIHMLQNFKIETNSMAEVKTTFDLILVPEKPILLTLRPINSSPHHHHHH

来源 Source

来源生物 organism	synthetic construct
NCBI 分类编号 ncbi_taxonomy_id	32630
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	1

Entity 3 non-polymer

描述 description	desmosterol
分子量 formula_weight	384.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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7. 引用文献 (1)

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晶胞边长 a length_a	156.034 Å
晶胞边长 b length_b	156.034 Å
晶胞边长 c length_c	156.034 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	24

空间群 space_group	I 21 3
空间群编号 int_tables_number	199
晶系 crystal_system	cubic

分辨率 resolution	2.900 Å
最低分辨率 resolution_low	39.010 Å
R 因子 r_factor	0.2096
R_work r_work	0.2070
R_free r_free	0.2613

fit	/app/data/saxs_computation/on/9onh/9onh.fit
pddf	/app/data/pr_computation/on/9onh/9onh.pr.out
profile	/app/data/saxs_computation/on/9onh/9onh.dat

Structure of ancestral-reconstructed cytochrome P450 11A1 (CYP11A1) in complex with desmosterol

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