9kd2

Crystal structure of Bacteroides ovatus DhuD complexed with NAD+ responsible for metabolism of glycosaminoglycan

Method: X-RAY DIFFRACTION D_max: 126.5 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	9kd2
沉积日期 deposition_date	2024-11-02
最后修订 last_revision	2025-10-29
结构标题 title	Crystal structure of Bacteroides ovatus DhuD complexed with NAD+ responsible for metabolism of glycosaminoglycan
关键词 keywords	Reductase, NAD+, Glycosaminoglycan metabolism, Bacteroides, 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	38.63 Å
回转半径 Rg (电子) rg_electron	38.27 Å
零角强度 I(0) i0	434438000.00
分子量 molecular_weight	169300.0 kDa
排除体积 excluded_volume	211550 Å³
包络体积 envelope_volume	262050 Å³
水化壳体积 shell_volume	56675 Å³
包络直径 envelope_diameter	137.0 Å
壳层 Rg shell_rg	44.52 Å
包络 Rg envelope_rg	38.07 Å
形状 Rg shape_rg	38.29 Å
总 Rg total_rg	38.55 Å
总原子数 total_atoms	11856
残基数 n_residues	1551
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	126.5 Å
Rg (实空间) rg_real	38.63 Å
Rg 误差 (实空间) rg_real_error	0.93 Å
I(0) (实空间) i0_real	4.3440e+08
I(0) 误差 (实空间) i0_real_error	6.6730e+06
Rg (倒空间) rg_reciprocal	38.63 Å
I(0) (倒空间) i0_reciprocal	434400000.0000
解质量估计 total_estimate	0.8938
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	43.2 Å
偏度 Skewness skewness	0.300
峰度 Kurtosis kurtosis	-0.541
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	87810000.0000
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: 0.904; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.908

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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	Oxidoreductase, short chain dehydrogenase/reductase family protein
分子量 formula_weight	29576.9 kDa
来源方法 src_method	man
拷贝数 entity_count	6

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F
原子数 atom_count	11858

MNQFLNFSLEGKVALVTGASYGIGFAIASAFAEQGAKVCFNDINQELVDKGMAAYAAKGIKAHGYVCDVTDEPAVQAMVATIAKEVGTIDILVNNAGIIRRVPMHEMDAADFRRVIDIDLNAPFIVAKAVLPAMMEKRAGKIINICSMMSELGRETVSAYAAAKGGLKMLTRNICSEYGEYNIQCNGIGPGYIATPQTAPLREPQADGSRHPFDSFICAKTPAGRWLDPEELTGPAVFLASEASNAVNGHILYVDGGILAYIGKQPKLEHHHHHH

来源 Source

来源生物 organism	Bacteroides ovatus ATCC 8483
NCBI 分类编号 ncbi_taxonomy_id	411476
宿主生物 host_organism	Escherichia coli B

Entity 2 non-polymer

描述 description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
分子量 formula_weight	663.4 kDa
来源方法 src_method	nat
拷贝数 entity_count	6

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	2

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7. 引用文献 (1)

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晶胞边长 a length_a	161.943 Å
晶胞边长 b length_b	126.911 Å
晶胞边长 c length_c	71.657 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	102.38 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	24

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	3.100 Å
最低分辨率 resolution_low	48.690 Å
R 因子 r_factor	0.1977
R_work r_work	0.1954
R_free r_free	0.2417

fit	/app/data/saxs_computation/kd/9kd2/9kd2.fit
pddf	/app/data/pr_computation/kd/9kd2/9kd2.pr.out
profile	/app/data/saxs_computation/kd/9kd2/9kd2.dat

Crystal structure of Bacteroides ovatus DhuD complexed with NAD+ responsible for metabolism of glycosaminoglycan

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