9npd

;Crystal structure of the inactive conformation of a glycoside hydrolase (CapGH2b - E553Q Mutant) from the GH2 family in the space group P3121 at 3.05 A ;

Method: X-RAY DIFFRACTION D_max: 124.3 Å Quality: REASONABLE

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

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	9npd
沉积日期 deposition_date	2025-03-11
结构标题 title	;Crystal structure of the inactive conformation of a glycoside hydrolase (CapGH2b - E553Q Mutant) from the GH2 family in the space group P3121 at 3.05 A ;
关键词 keywords	Redox-regulation, glycosyl hydrolase, mannosidase, redox-switch, metagenome, disulfide bond, HYDROLASE; HYDROLASE
实验方法 method	X-RAY DIFFRACTION

▼

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	42.82 Å
回转半径 Rg (电子) rg_electron	42.40 Å
零角强度 I(0) i0	940762000.00
分子量 molecular_weight	253010.0 kDa
排除体积 excluded_volume	315810 Å³
包络体积 envelope_volume	408200 Å³
水化壳体积 shell_volume	76943 Å³
包络直径 envelope_diameter	127.2 Å
壳层 Rg shell_rg	50.52 Å
包络 Rg envelope_rg	41.65 Å
形状 Rg shape_rg	42.38 Å
总 Rg total_rg	42.83 Å
总原子数 total_atoms	17839
残基数 n_residues	2212
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

▼

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	124.3 Å
Rg (实空间) rg_real	42.59 Å
Rg 误差 (实空间) rg_real_error	0.77 Å
I(0) (实空间) i0_real	9.4080e+08
I(0) 误差 (实空间) i0_real_error	1.6380e+07
Rg (倒空间) rg_reciprocal	42.82 Å
I(0) (倒空间) i0_reciprocal	941000000.0000
解质量估计 total_estimate	0.6457
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	53.7 Å
偏度 Skewness skewness	0.059
峰度 Kurtosis kurtosis	-0.677
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	100100000.0000
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: 0.991; Stabil: 1.000; Sysdev: 0.016; Positv: 1.000; Valcen: 0.990; Smooth: 0.377

▶

4. 晶体学与实验 4. Crystallography & Experiment

▶

5. 实体与聚合体信息 (5)

Entity 1 polymer

描述 description	Glycoside hydrolase family 2
分子量 formula_weight	90815.6 kDa
EC 编号 ec_number	3.2.1.25
突变 mutation	E553Q
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	17910

MGSSHHHHHHSSGLVPRGSHMFVSEQSLNGRWTLKFFPQPAVPVMTIEGAEAANGIVVDAVVPGNVEIDMEAAGLVEDPMVGNNIYKLRPYEGYQWYYSRTFAAPVVTEGQRLVLHFGGIDTFAEVYVNGIKVGSADNMLIEHDYDITSVVKEGENRLDVIIRSSVMEAQNHFLGTLSIGNFSNEESAPVRRAPSTYGWDIMPRLVSAGLWRDVTLRVENPVTIVDANWVTLSVNPKAREASESLYLQTRLPFEMHDKVKAVITISRDGRQILRKEALMRKFANLFTLNLSGVDAWWPRGYGEPALYTAEVSLVDVTSGKIYDTKTSKIGFRTVKLELDEVNLPGQPGQFQFIINGEPVFAKGTNWVPLDALHSRDASHVEEAVQLMVEMNCNIVRCWGGNVYEDTHFFELCDKYGIMVWQDFAMGCGNYSQRDNFAAALEKEAISVVVKLRNHPSLILWSGNNEDDQSLVFGRLAPFKANPNNDRVSRQVLSRVIYEFDPTRPYLPSSPYYGPKVCEVGVRDEVLPENHLWGPRGYYKDPFYTENPSQFVSQIGYHGCPNRETLERMFSPDSVNPWQNGVVGMWNDEWQTKANRIYDDKFQGGRNDLMTNQVRIIFGEVPADLDDFIFASQSVQAEAMKFFVELWRGRRPYRTGIIWWNIRDGWPLLSDAISDYWGGKKQAFYYMQNVHHDVCCLINPAANGYMLKVDNNTLKDFEGVVEVKDVASGKQVFKGKFVSKANQMSEIATLPMQKGQGMLVISYRIEGNEYFNHYLYGEPPYKLDQYRKWVKKCGIYELE

来源 Source

来源生物 organism	metagenome
NCBI 分类编号 ncbi_taxonomy_id	256318
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

描述 description	PHOSPHATE ION
分子量 formula_weight	95.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	10

Entity 3 non-polymer

描述 description	ACETATE ION
分子量 formula_weight	59.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 4 non-polymer

描述 description	MALONATE ION
分子量 formula_weight	102.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 5 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	71

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	222.906 Å
晶胞边长 b length_b	222.906 Å
晶胞边长 c length_c	151.360 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	120.00 °
晶胞分子数 Z z_pdb	18

空间群 space_group	P 31 2 1
空间群编号 int_tables_number	152
晶系 crystal_system	—

分辨率 resolution	3.050 Å
最低分辨率 resolution_low	49.020 Å
R 因子 r_factor	0.2186
R_work r_work	0.2175
R_free r_free	0.2385

fit	/app/data/saxs_computation/np/9npd/9npd.fit
pddf	/app/data/pr_computation/np/9npd/9npd.pr.out
profile	/app/data/saxs_computation/np/9npd/9npd.dat

;Crystal structure of the inactive conformation of a glycoside hydrolase (CapGH2b - E553Q Mutant) from the GH2 family in the space group P3121 at 3.05 A ;

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