8ibt

;Crystal structure of GH42 beta-galactosidase BiBga42A from Bifidobacterium longum subspecies infantis E318S mutant in complex with lacto-N-tetraose ;

Method: X-RAY DIFFRACTION D_max: 120.9 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

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8ibt
沉积日期 deposition_date	2023-02-10
结构标题 title	;Crystal structure of GH42 beta-galactosidase BiBga42A from Bifidobacterium longum subspecies infantis E318S mutant in complex with lacto-N-tetraose ;
关键词 keywords	Glycoside Hydrolase family 42, 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	37.41 Å
回转半径 Rg (电子) rg_electron	36.75 Å
零角强度 I(0) i0	378591000.00
分子量 molecular_weight	156470.0 kDa
排除体积 excluded_volume	194450 Å³
包络体积 envelope_volume	244610 Å³
水化壳体积 shell_volume	54324 Å³
包络直径 envelope_diameter	127.1 Å
壳层 Rg shell_rg	43.98 Å
包络 Rg envelope_rg	36.48 Å
形状 Rg shape_rg	36.76 Å
总 Rg total_rg	37.15 Å
总原子数 total_atoms	11061
残基数 n_residues	1387
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	120.9 Å
Rg (实空间) rg_real	37.33 Å
Rg 误差 (实空间) rg_real_error	0.89 Å
I(0) (实空间) i0_real	3.7860e+08
I(0) 误差 (实空间) i0_real_error	6.2340e+06
Rg (倒空间) rg_reciprocal	37.38 Å
I(0) (倒空间) i0_reciprocal	378600000.0000
解质量估计 total_estimate	0.6874
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	46.1 Å
偏度 Skewness skewness	0.245
峰度 Kurtosis kurtosis	-0.525
角度范围 angular_range	— – 0.2100 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	123800000.0000
实空间数据点数 n_real_points	43
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.925; Stabil: 1.000; Sysdev: 0.080; Positv: 1.000; Valcen: 1.000; Smooth: 0.915

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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	Beta-galactosidase
分子量 formula_weight	78764.8 kDa
EC 编号 ec_number	3.2.1.23
突变 mutation	E318S
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	11711

MEHRAFKWPQPLAGNKPRIWYGGDYNPDQWPEEVWDEDVALMQQAGVNLVSVAIFSWAKLEPEEGVYDFDWLDRVIDKLGKAGIAVDLASGTASPPMWMTQAHPEILWVDYRGDVCQPGARQHWRATSPVFLDYALNLCRKMAEHYKDNPYVVSWHVSNEYGCHNRFDYSEDAERAFQKWCEKKYGTIDAVNDAWGTAFWAQRMNNFSEIIPPRFIGDGNFMNPGKLLDWKRFSSDALLDFYKAERDALLEIAPKPQTTNFMVSAGCTVLDYDKWGHDVDFVSNDHYFSPGEAHFDEMAYAACLTDGIARKNPWFLMSHSTSAVNWRPTNYRLEPGELVRDSLAHLAMGADAICYFQWRQSKAGAEKWHSAMVPHAGPDSQIFRDVCELGADLNKLADEGLLSTKLVKSKVAIVFDYESQWATEHTATPTQEVRHWTEPLDWFRALADNGLTADVVPVRGPWDEYEAVVLPSLAILSEQTTRRVREYVANGGKLFVTYYTGLVDDRDHVWLGGYPGSIRDVVGVRVEEFAPMGTDAPGTMDHLDLDNGTVAHDFADVITSVADTAHVVASFKADKWTGFDGAPAITVNDFGDGKAAYVGARLGREGLAKSLPALLEELGIETSAEDDRGEVLRVERADETGENHFVFLFNRTHDVAVVDVEGEPLVASLAQVNESEHTAAIQPNGVLVVKLAAALEHHHHHH

来源 Source

来源生物 organism	Bifidobacterium longum subsp. infantis (strain ATCC 15697 / DSM 20088 / JCM 1222 / NCTC 11817 / S12)
NCBI 分类编号 ncbi_taxonomy_id	391904
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 branched

描述 description	beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose
分子量 formula_weight	707.6 kDa
来源方法 src_method	man
拷贝数 entity_count	2

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	650

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7. 引用文献 (2)

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晶胞边长 a length_a	166.432 Å
晶胞边长 b length_b	166.432 Å
晶胞边长 c length_c	149.459 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	12

空间群 space_group	P 3 2 1
空间群编号 int_tables_number	150
晶系 crystal_system	—

分辨率 resolution	2.200 Å
最低分辨率 resolution_low	48.040 Å
R 因子 r_factor	0.1477
R_work r_work	0.1463
R_free r_free	0.1749

fit	/app/data/saxs_computation/ib/8ibt/8ibt.fit
pddf	/app/data/pr_computation/ib/8ibt/8ibt.pr.out
profile	/app/data/saxs_computation/ib/8ibt/8ibt.dat

;Crystal structure of GH42 beta-galactosidase BiBga42A from Bifidobacterium longum subspecies infantis E318S mutant in complex with lacto-N-tetraose ;

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