8k2n

;Crystal structure of Group 4 Monosaccharide-releasing beta-N-acetylgalactosaminidase NgaLy from Lacticaseibacillus yichunensis, apo form ;

Method: X-RAY DIFFRACTION D_max: 138.1 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	8k2n
沉积日期 deposition_date	2023-07-12
结构标题 title	;Crystal structure of Group 4 Monosaccharide-releasing beta-N-acetylgalactosaminidase NgaLy from Lacticaseibacillus yichunensis, apo form ;
关键词 keywords	Glycoside hydrolase, HYDROLASE; HYDROLASE
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	43.21 Å
回转半径 Rg (电子) rg_electron	43.01 Å
零角强度 I(0) i0	795985000.00
分子量 molecular_weight	240400.0 kDa
排除体积 excluded_volume	303360 Å³
包络体积 envelope_volume	388810 Å³
水化壳体积 shell_volume	74851 Å³
包络直径 envelope_diameter	142.5 Å
壳层 Rg shell_rg	48.18 Å
包络 Rg envelope_rg	42.60 Å
形状 Rg shape_rg	43.00 Å
总 Rg total_rg	43.30 Å
总原子数 total_atoms	17040
残基数 n_residues	2173
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	138.1 Å
Rg (实空间) rg_real	43.15 Å
Rg 误差 (实空间) rg_real_error	0.91 Å
I(0) (实空间) i0_real	7.9600e+08
I(0) 误差 (实空间) i0_real_error	1.4170e+07
Rg (倒空间) rg_reciprocal	43.21 Å
I(0) (倒空间) i0_reciprocal	796000000.0000
解质量估计 total_estimate	0.8826
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	52.3 Å
偏度 Skewness skewness	0.283
峰度 Kurtosis kurtosis	-0.466
角度范围 angular_range	— – 0.1850 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	213700000.0000
实空间数据点数 n_real_points	38
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.926; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.695

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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 (2)

Entity 1 polymer

描述 description	Monosaccharide-releasing beta-N-acetylgalactosaminidase
分子量 formula_weight	61083.9 kDa
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	D,C,A,B
原子数 atom_count	17554

GPGMDYQIDLVDPLTKVFADEVPDAWVVATQMVLQGEPLVLQLAYQRLRDDDASFSELTLATSLSAQCFEINQVPSQLPTWPHPDARYLRTTPGLFPDLLTPLTGPVRAYHGQVRALWLKIPTESLTPGSYELTITLTETASGQVVFSQTVPLTVAAAVAQPPRLHHTEWFSVDCLADYYHEAPYTPRLWAIIGNFMVFAHDEALMDTLLTPIFTPPLDTAVGATRTNVQLVQILPGTPYRFDWSRLRKWCQLAQQSGFAYLEMPPLFTQWGAQATPTITDTAGTALFGWHVPSTAPAYRAFLQALLPQLLAVLAEEGYDRDHLFFHLADEPNASTEDGYRAARAQVADLLDGLQVIDALSDVRFYENGLVPHPVVADDALAPFLAADAAPLWTYYCCAQTTAVPNRFFALRSYDNRVLGVLLYRHQIQGFLHWGFNFYNAQLSTRPIDPFAVTDAGGAFPSGDPFLVYPGADGQPLNSLRNEVQRLGFGDLAVLQQLEALKGRPFVERLIDVTAGMVPQFDDYPPDAGWLTRLHEKAVATLAAAAPAHKKE

来源 Source

来源生物 organism	Lacticaseibacillus yichunensis
NCBI 分类编号 ncbi_taxonomy_id	2486015
宿主生物 host_organism	Escherichia coli

Entity 2 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	514

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7. 引用文献 (1)

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晶胞边长 a length_a	82.930 Å
晶胞边长 b length_b	94.620 Å
晶胞边长 c length_c	116.180 Å
晶胞夹角 α angle_alpha	70.93 °
晶胞夹角 β angle_beta	73.81 °
晶胞夹角 γ angle_gamma	72.43 °
晶胞分子数 Z z_pdb	4

空间群 space_group	P 1
空间群编号 int_tables_number	1
晶系 crystal_system	—

分辨率 resolution	2.500 Å
最低分辨率 resolution_low	48.790 Å
R 因子 r_factor	0.1856
R_work r_work	0.1827
R_free r_free	0.2415

fit	/app/data/saxs_computation/k2/8k2n/8k2n.fit
pddf	/app/data/pr_computation/k2/8k2n/8k2n.pr.out
profile	/app/data/saxs_computation/k2/8k2n/8k2n.dat

;Crystal structure of Group 4 Monosaccharide-releasing beta-N-acetylgalactosaminidase NgaLy from Lacticaseibacillus yichunensis, apo form ;

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

5. 实体与聚合体信息 (2)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 water

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)