8yvr

Crystal structure of GH65 alpha-1,2-glucosidase from Flavobacterium johnsoniae in complex with 1-deoxynojirimycin

Method: X-RAY DIFFRACTION D_max: 123.4 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	8yvr
沉积日期 deposition_date	2024-03-29
最后修订 last_revision	2025-03-19
结构标题 title	Crystal structure of GH65 alpha-1,2-glucosidase from Flavobacterium johnsoniae in complex with 1-deoxynojirimycin
关键词 keywords	glycoside hydrolase, GH65, kojibiose, (alpha/alpha)6-barrel, inhibitor, glucosidase, dextran, 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	39.49 Å
回转半径 Rg (电子) rg_electron	38.79 Å
零角强度 I(0) i0	725114000.00
分子量 molecular_weight	223710.0 kDa
排除体积 excluded_volume	280630 Å³
包络体积 envelope_volume	341480 Å³
水化壳体积 shell_volume	70158 Å³
包络直径 envelope_diameter	127.0 Å
壳层 Rg shell_rg	47.19 Å
包络 Rg envelope_rg	38.50 Å
形状 Rg shape_rg	38.78 Å
总 Rg total_rg	39.24 Å
总原子数 total_atoms	31301
残基数 n_residues	1977
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	123.4 Å
Rg (实空间) rg_real	39.25 Å
Rg 误差 (实空间) rg_real_error	0.81 Å
I(0) (实空间) i0_real	7.2510e+08
I(0) 误差 (实空间) i0_real_error	1.1350e+07
Rg (倒空间) rg_reciprocal	39.40 Å
I(0) (倒空间) i0_reciprocal	725200000.0000
解质量估计 total_estimate	0.8982
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	52.5 Å
偏度 Skewness skewness	0.136
峰度 Kurtosis kurtosis	-0.550
角度范围 angular_range	— – 0.2000 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	336400000.0000
实空间数据点数 n_real_points	41
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.932; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.888

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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	Candidate alpha glycoside phosphorylase Glycoside hydrolase family 65
分子量 formula_weight	76489.2 kDa
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	32187

MGSSHHHHHHSSGLVPRGSHQDPWKLSADKPDSNNYYGETVANGMIGIISSPEPLKVKEVVLAGTYDIYKRGRVSSFIPNYNLLNMKLAFNGESVQTYNINNYKQELDMRNGAFTGSFQFKDLATVTYSYYALRHLPHCIMMVVNINTQKDTEINVENLLETPSSLNNQQNYFQNITNTHVNIPLLTSVAFTPTGRSKIAVSNTFLFDEGKKLQPEILHRMNDADMHAMSFDKKIKAGKTYSFALIGSLISSDHINDPYNEAERLTIYAALEGKSRLLNRHMQEWNSLWQSDIQVEGDPQAQQDIRSMLYHLYSFTRKSTSLSPSPMGLSGLGYNGHVFWDTEIWMFPPMLLLHPEIAKSMIEYRYQRLDAARKKAAIYGYDGAMFPWESADSGAEETPVNALTGAFEHHVTGDVAIAAWQYYLVTGDKEWLKEKGWPILKATAEFWASRVEKNDKGEYEIKNVVAADEWAENIDNNAYTNGTAIRNLQYASKCATVLGVIAPKEWTLIADKILISKMSNGVTREHDSYTDQNIKQADANLLAYPLKLITDKEQIERDLKYYQTKIPQSDTPAMTQAIFSLLYSRLEDSDQAYHWFKDAYQPNLNPPFRVISECKGGTNPYFSTGAGGVLQAVIMGFGGLDIDAAGGIKQVKSVLPKNWKKLTITGIGIEKKTFVLTH

来源 Source

来源生物 organism	Flavobacterium johnsoniae UW101
NCBI 分类编号 ncbi_taxonomy_id	376686
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

描述 description	1-DEOXYNOJIRIMYCIN
分子量 formula_weight	163.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 3 non-polymer

描述 description	1,2-ETHANEDIOL
分子量 formula_weight	62.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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	886

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7. 引用文献 (1)

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晶胞边长 a length_a	122.841 Å
晶胞边长 b length_b	194.371 Å
晶胞边长 c length_c	112.129 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	116.54 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	12

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	1.900 Å
最低分辨率 resolution_low	48.640 Å
R 因子 r_factor	—
R_work r_work	0.2539
R_free r_free	0.2762

fit	/app/data/saxs_computation/yv/8yvr/8yvr.fit
pddf	/app/data/pr_computation/yv/8yvr/8yvr.pr.out
profile	/app/data/saxs_computation/yv/8yvr/8yvr.dat

Crystal structure of GH65 alpha-1,2-glucosidase from Flavobacterium johnsoniae in complex with 1-deoxynojirimycin

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