9i2z

Alpha-Methylacyl-CoA racemase from Mycobacterium tuberculosis in complex with 2-methyldecanoyl-CoA

Method: X-RAY DIFFRACTION D_max: 185.2 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	9i2z
沉积日期 deposition_date	2025-01-22
结构标题 title	Alpha-Methylacyl-CoA racemase from Mycobacterium tuberculosis in complex with 2-methyldecanoyl-CoA
关键词 keywords	CoA-transferase, epimerization, CoA-transferase family III, alpha proton exchange, homo dimer, ISOMERASE, 2-methyldecanoyl-CoA; ISOMERASE
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	58.02 Å
回转半径 Rg (电子) rg_electron	57.74 Å
零角强度 I(0) i0	6564540000.00
分子量 molecular_weight	441140.0 kDa
排除体积 excluded_volume	420630 Å³
包络体积 envelope_volume	783260 Å³
水化壳体积 shell_volume	110940 Å³
包络直径 envelope_diameter	185.8 Å
壳层 Rg shell_rg	61.67 Å
包络 Rg envelope_rg	56.52 Å
形状 Rg shape_rg	57.74 Å
总 Rg total_rg	57.81 Å
总原子数 total_atoms	33256
残基数 n_residues	4304
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	185.2 Å
Rg (实空间) rg_real	57.86 Å
Rg 误差 (实空间) rg_real_error	1.51 Å
I(0) (实空间) i0_real	6.5650e+09
I(0) 误差 (实空间) i0_real_error	1.3180e+08
Rg (倒空间) rg_reciprocal	58.13 Å
I(0) (倒空间) i0_reciprocal	6567000000.0000
解质量估计 total_estimate	0.8652
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	75.5 Å
偏度 Skewness skewness	0.157
峰度 Kurtosis kurtosis	-0.552
角度范围 angular_range	— – 0.1350 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	432600000.0000
实空间数据点数 n_real_points	28
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.916; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.496

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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	Alpha-methylacyl-CoA racemase
分子量 formula_weight	39027.1 kDa
EC 编号 ec_number	5.1.99.4
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	34951

MAGPLSGLRVVELAGIGPGPHAAMILGDLGADVVRIDRPSSVDGISRDAMLRNRRIVTADLKSDQGLELALKLIAKADVLIEGYRPGVTERLGLGPEECAKVNDRLIYARMTGWGQTGPRSQQAGHDINYISLNGILHAIGRGDERPVPPLNLVGDFGGGSMFLLVGILAALWERQSSGKGQVVDAAMVDGSSVLIQMMWAMRATGMWTDTRGANMLDGGAPYYDTYECADGRYVAVGAIEPQFYAAMLAGLGLDAAELPPQNDRARWPELRALLTEAFASHDRDHWGAVFANSDACVTPVLAFGEVHNEPHIIERNTFYEANGGWQPMPAPRFSRTASSQPRPPAATIDIEAVLTDWDGGSGC

来源 Source

来源生物 organism	Mycobacterium tuberculosis
NCBI 分类编号 ncbi_taxonomy_id	1773
宿主生物 host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 non-polymer

描述 description	(S)-2-methyldecanoyl-CoA
分子量 formula_weight	935.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	12

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	1668

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7. 引用文献 (1)

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晶胞边长 a length_a	277.034 Å
晶胞边长 b length_b	277.034 Å
晶胞边长 c length_c	390.861 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	192

空间群 space_group	I 4 2 2
空间群编号 int_tables_number	97
晶系 crystal_system	—

分辨率 resolution	2.110 Å
最低分辨率 resolution_low	226.019 Å
R 因子 r_factor	—
R_work r_work	0.2010
R_free r_free	0.2390

fit	/app/data/saxs_computation/i2/9i2z/9i2z.fit
pddf	/app/data/pr_computation/i2/9i2z/9i2z.pr.out
profile	/app/data/saxs_computation/i2/9i2z/9i2z.dat

Alpha-Methylacyl-CoA racemase from Mycobacterium tuberculosis in complex with 2-methyldecanoyl-CoA

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