8ibr

Crystal structure of GH42 beta-galactosidase BiBga42A from Bifidobacterium longum subspecies infantis in complex with glycerol

Method: X-RAY DIFFRACTION D_max: 83.5 Å Quality: EXCELLENT

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	8ibr
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 in complex with glycerol
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	27.28 Å
回转半径 Rg (电子) rg_electron	26.14 Å
零角强度 I(0) i0	99902200.00
分子量 molecular_weight	77575.0 kDa
排除体积 excluded_volume	96413 Å³
包络体积 envelope_volume	114470 Å³
水化壳体积 shell_volume	35274 Å³
包络直径 envelope_diameter	89.5 Å
壳层 Rg shell_rg	34.61 Å
包络 Rg envelope_rg	26.31 Å
形状 Rg shape_rg	26.14 Å
总 Rg total_rg	27.01 Å
总原子数 total_atoms	5485
残基数 n_residues	691
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	83.5 Å
Rg (实空间) rg_real	27.14 Å
Rg 误差 (实空间) rg_real_error	0.39 Å
I(0) (实空间) i0_real	9.9900e+07
I(0) 误差 (实空间) i0_real_error	1.3110e+06
Rg (倒空间) rg_reciprocal	27.19 Å
I(0) (倒空间) i0_reciprocal	99910000.0000
解质量估计 total_estimate	0.9088
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	33.1 Å
偏度 Skewness skewness	0.198
峰度 Kurtosis kurtosis	-0.501
角度范围 angular_range	— – 0.2900 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	25640000.0000
实空间数据点数 n_real_points	59
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.949; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.971

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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	Beta-galactosidase
分子量 formula_weight	78806.9 kDa
EC 编号 ec_number	3.2.1.23
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	6160

MEHRAFKWPQPLAGNKPRIWYGGDYNPDQWPEEVWDEDVALMQQAGVNLVSVAIFSWAKLEPEEGVYDFDWLDRVIDKLGKAGIAVDLASGTASPPMWMTQAHPEILWVDYRGDVCQPGARQHWRATSPVFLDYALNLCRKMAEHYKDNPYVVSWHVSNEYGCHNRFDYSEDAERAFQKWCEKKYGTIDAVNDAWGTAFWAQRMNNFSEIIPPRFIGDGNFMNPGKLLDWKRFSSDALLDFYKAERDALLEIAPKPQTTNFMVSAGCTVLDYDKWGHDVDFVSNDHYFSPGEAHFDEMAYAACLTDGIARKNPWFLMEHSTSAVNWRPTNYRLEPGELVRDSLAHLAMGADAICYFQWRQSKAGAEKWHSAMVPHAGPDSQIFRDVCELGADLNKLADEGLLSTKLVKSKVAIVFDYESQWATEHTATPTQEVRHWTEPLDWFRALADNGLTADVVPVRGPWDEYEAVVLPSLAILSEQTTRRVREYVANGGKLFVTYYTGLVDDRDHVWLGGYPGSIRDVVGVRVEEFAPMGTDAPGTMDHLDLDNGTVAHDFADVITSVADTAHVVASFKADKWTGFDGAPAITVNDFGDGKAAYVGARLGREGLAKSLPALLEELGIETSAEDDRGEVLRVERADETGENHFVFLFNRTHDVAVVDVEGEPLVASLAQVNESEHTAAIQPNGVLVVKLAAALEHHHHHH

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 non-polymer

描述 description	GLYCEROL
分子量 formula_weight	92.1 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

Entity 3 non-polymer

描述 description	DI(HYDROXYETHYL)ETHER
分子量 formula_weight	106.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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	670

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7. 引用文献 (2)

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晶胞边长 a length_a	145.642 Å
晶胞边长 b length_b	145.642 Å
晶胞边长 c length_c	66.845 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	6

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	1.700 Å
最低分辨率 resolution_low	45.910 Å
R 因子 r_factor	0.1623
R_work r_work	0.1611
R_free r_free	0.1857

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

Crystal structure of GH42 beta-galactosidase BiBga42A from Bifidobacterium longum subspecies infantis in complex with glycerol

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