9o8y

;Crystal structure of 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase (DapD) from Bordetella pertussis (succinyl-CoA bound) ;

Method: X-RAY DIFFRACTION D_max: 81.3 Å Quality: EXCELLENT

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	9o8y
沉积日期 deposition_date	2025-04-17
最后修订 last_revision	2025-04-30
结构标题 title	;Crystal structure of 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase (DapD) from Bordetella pertussis (succinyl-CoA bound) ;
关键词 keywords	SSGCID, STRUCTURAL GENOMICS, SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE, dapD, Bordetella pertussis, TRANSFERASE; TRANSFERASE
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	27.32 Å
回转半径 Rg (电子) rg_electron	25.98 Å
零角强度 I(0) i0	112493000.00
分子量 molecular_weight	83148.0 kDa
排除体积 excluded_volume	103920 Å³
包络体积 envelope_volume	122130 Å³
水化壳体积 shell_volume	37653 Å³
包络直径 envelope_diameter	84.6 Å
壳层 Rg shell_rg	34.65 Å
包络 Rg envelope_rg	26.22 Å
形状 Rg shape_rg	25.99 Å
总 Rg total_rg	26.79 Å
总原子数 total_atoms	5845
残基数 n_residues	778
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	81.3 Å
Rg (实空间) rg_real	27.12 Å
Rg 误差 (实空间) rg_real_error	0.42 Å
I(0) (实空间) i0_real	1.1250e+08
I(0) 误差 (实空间) i0_real_error	1.3850e+06
Rg (倒空间) rg_reciprocal	27.18 Å
I(0) (倒空间) i0_reciprocal	112500000.0000
解质量估计 total_estimate	0.9088
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	35.0 Å
偏度 Skewness skewness	0.097
峰度 Kurtosis kurtosis	-0.533
角度范围 angular_range	— – 0.2900 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	24500000.0000
实空间数据点数 n_real_points	59
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.955; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.966

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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	2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
分子量 formula_weight	29967.0 kDa
EC 编号 ec_number	2.3.1.117
来源方法 src_method	man
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C
原子数 atom_count	6597

MAHHHHHHTLDLQTTIEQAWENRANLSPVDASAEVRDAVEHTIDGLDLGRLRVAEKIDDQWIVHQWIKKAVLLSFRLHDNAVMGQGPLQFYDKVPTKFAGYGEAAFKAGGYRVVPPAVARRGAFIARNVVLMPSYVNIGAYVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANPTIIEDNCFIGARSEVVEGVVVEENSVLAMGVFLSQSTKIYDRATGKVSYGRVPSGSVVVPGSLPSEDGSHSLACAVIVKRVDAQTRAKTSINDLL

来源 Source

来源生物 organism	Bordetella pertussis Tohama I
NCBI 分类编号 ncbi_taxonomy_id	257313
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

描述 description	CHLORIDE ION
分子量 formula_weight	35.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	5

Entity 3 non-polymer

描述 description	SUCCINYL-COENZYME A
分子量 formula_weight	867.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 4 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	686

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7. 引用文献 (1)

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晶胞边长 a length_a	86.264 Å
晶胞边长 b length_b	88.645 Å
晶胞边长 c length_c	117.291 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	12

空间群 space_group	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	1.450 Å
最低分辨率 resolution_low	48.910 Å
R 因子 r_factor	0.1605
R_work r_work	0.1593
R_free r_free	0.1824

fit	/app/data/saxs_computation/o8/9o8y/9o8y.fit
pddf	/app/data/pr_computation/o8/9o8y/9o8y.pr.out
profile	/app/data/saxs_computation/o8/9o8y/9o8y.dat

;Crystal structure of 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase (DapD) from Bordetella pertussis (succinyl-CoA bound) ;

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