9m2a

The crystal structure of the trypanosome alternative oxidase complexed with a trypanocidal phosphonium derivative (compound1)

Method: X-RAY DIFFRACTION D_max: 132.8 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	9m2a
沉积日期 deposition_date	2025-02-27
最后修订 last_revision	2025-09-10
结构标题 title	The crystal structure of the trypanosome alternative oxidase complexed with a trypanocidal phosphonium derivative (compound1)
关键词 keywords	ALTERNATIVE OXIDASE, INHIBITOR, DRUG, AFRICAN TRYPANOSOMES, 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	38.52 Å
回转半径 Rg (电子) rg_electron	38.96 Å
零角强度 I(0) i0	456659000.00
分子量 molecular_weight	116280.0 kDa
排除体积 excluded_volume	112500 Å³
包络体积 envelope_volume	199590 Å³
水化壳体积 shell_volume	44920 Å³
包络直径 envelope_diameter	137.0 Å
壳层 Rg shell_rg	41.73 Å
包络 Rg envelope_rg	39.04 Å
形状 Rg shape_rg	38.99 Å
总 Rg total_rg	39.03 Å
总原子数 total_atoms	8805
残基数 n_residues	1078
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	132.8 Å
Rg (实空间) rg_real	39.03 Å
Rg 误差 (实空间) rg_real_error	1.22 Å
I(0) (实空间) i0_real	4.5670e+08
I(0) 误差 (实空间) i0_real_error	7.1280e+06
Rg (倒空间) rg_reciprocal	38.72 Å
I(0) (倒空间) i0_reciprocal	456500000.0000
解质量估计 total_estimate	0.5570
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	32.4 Å
偏度 Skewness skewness	0.552
峰度 Kurtosis kurtosis	-0.457
角度范围 angular_range	— – 0.2050 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	107800000.0000
实空间数据点数 n_real_points	42
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.612; Stabil: 1.000; Sysdev: 0.035; Positv: 1.000; Valcen: 0.676; Smooth: 0.621

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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 (4)

Entity 1 polymer

描述 description	Alternative oxidase, mitochondrial
分子量 formula_weight	31372.3 kDa
EC 编号 ec_number	1.-.-.-
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	8805

AAVWGHTQLNRLSFLETVPVVPLRVSDESSEDRPTWSLPDIENVAITHKKPNGLVDTLAYRSVRTCRWLFDTFSLYRFGSITESKVISRCLFLETVAGVPGMVGGMLRHLSSLRYMTRDKGWINTLLVEAENERMHLMTFIELRQPGLPLRVSIIITQAIMYLFLLVAYVISPRFVHRFVGYLEEEAVITYTGVMRAIDEGRLRPTKNDVPEVARVYWNLSKNATFRDLINVIRADEAEHRVVNHTFADMHEKRLQNSVNPFVVLKKNPEEM

来源 Source

来源生物 organism	Trypanosoma brucei brucei
NCBI 分类编号 ncbi_taxonomy_id	5702
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	FE (III) ION
分子量 formula_weight	55.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	8

Entity 3 non-polymer

描述 description	HYDROXIDE ION
分子量 formula_weight	17.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 4 non-polymer

描述 description	14-[diphenyl(pyridin-2-yl)-$l^{5}-phosphanyl]tetradecyl 2-methyl-4-oxidanyl-benzoate
分子量 formula_weight	611.8 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	151.368 Å
晶胞边长 b length_b	221.727 Å
晶胞边长 c length_c	62.855 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	114.50 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	16

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	—

分辨率 resolution	3.010 Å
最低分辨率 resolution_low	44.960 Å
R 因子 r_factor	0.1975
R_work r_work	0.1945
R_free r_free	0.2535

fit	/app/data/saxs_computation/m2/9m2a/9m2a.fit
pddf	/app/data/pr_computation/m2/9m2a/9m2a.pr.out
profile	/app/data/saxs_computation/m2/9m2a/9m2a.dat

The crystal structure of the trypanosome alternative oxidase complexed with a trypanocidal phosphonium derivative (compound1)

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