9iqb

Crystal structure of beta-glucosidase from Acetivibrio thermocellus

Method: X-RAY DIFFRACTION D_max: 191.1 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	9iqb
沉积日期 deposition_date	2024-07-12
结构标题 title	Crystal structure of beta-glucosidase from Acetivibrio thermocellus
关键词 keywords	Beta-glucosidase, GH1 family, Cellobiose, 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	63.84 Å
回转半径 Rg (电子) rg_electron	63.03 Å
零角强度 I(0) i0	4935680000.00
分子量 molecular_weight	619020.0 kDa
排除体积 excluded_volume	782340 Å³
包络体积 envelope_volume	1180100 Å³
水化壳体积 shell_volume	149210 Å³
包络直径 envelope_diameter	185.0 Å
壳层 Rg shell_rg	74.12 Å
包络 Rg envelope_rg	59.03 Å
形状 Rg shape_rg	63.00 Å
总 Rg total_rg	63.31 Å
总原子数 total_atoms	43912
残基数 n_residues	5388
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	191.1 Å
Rg (实空间) rg_real	63.13 Å
Rg 误差 (实空间) rg_real_error	1.89 Å
I(0) (实空间) i0_real	4.9360e+09
I(0) 误差 (实空间) i0_real_error	1.0460e+08
Rg (倒空间) rg_reciprocal	64.41 Å
I(0) (倒空间) i0_reciprocal	4946000000.0000
解质量估计 total_estimate	0.8653
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	91.7 Å
偏度 Skewness skewness	-0.174
峰度 Kurtosis kurtosis	-0.583
角度范围 angular_range	— – 0.1250 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	146500000.0000
实空间数据点数 n_real_points	26
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.854; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.940; Smooth: 0.742

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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-glucosidase A
分子量 formula_weight	52618.3 kDa
EC 编号 ec_number	3.2.1.21
来源方法 src_method	man
拷贝数 entity_count	12

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F,G,H,I,J,K,L
原子数 atom_count	44214

MSKITFPKDFIWGSATAAYQIEGAYNEDGKGESIWDRFSHTPGNIADGHTGDVACDHYHRYEEDIKIMKEIGIKSYRFSISWPRIFPEGTGKLNQKGLDFYKRLTNLLLENGIMPAITLYHWDLPQKLQDKGGWKNRDTTDYFTEYSEVIFKNLGDIVPIWFTHNEPGVVSLLGHFLGIHAPGIKDLRTSLEVSHNLLLSHGKAVKLFREMNIDAQIGIALNLSYHYPASEKAEDIEAAELSFSLAGRWYLDPVLKGRYPENALKLYKKKGIELSFPEDDLKLISQPIDFIAFNNYSSEFIKYDPSSESGFSPANSILEKFEKTDMGWIIYPEGLYDLLMLLDRDYGKPNIVISENGAAFKDEIGSNGKIEDTKRIQYLKDYLTQAHRAIQDGVNLKAYYLWSLLDNFEWAYGYNKRFGIVHVNFDTLERKIKDSGYWYKEVIKNNGFLEHHHHHH

来源 Source

来源生物 organism	Acetivibrio thermocellus
NCBI 分类编号 ncbi_taxonomy_id	1515
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

描述 description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
分子量 formula_weight	122.1 kDa
来源方法 src_method	syn
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	302

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7. 引用文献 (1)

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晶胞边长 a length_a	109.930 Å
晶胞边长 b length_b	158.620 Å
晶胞边长 c length_c	158.910 Å
晶胞夹角 α angle_alpha	60.12 °
晶胞夹角 β angle_beta	88.19 °
晶胞夹角 γ angle_gamma	87.48 °
晶胞分子数 Z z_pdb	12

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

分辨率 resolution	3.000 Å
最低分辨率 resolution_low	34.991 Å
R 因子 r_factor	—
R_work r_work	0.3000
R_free r_free	0.3500

fit	/app/data/saxs_computation/iq/9iqb/9iqb.fit
pddf	/app/data/pr_computation/iq/9iqb/9iqb.pr.out
profile	/app/data/saxs_computation/iq/9iqb/9iqb.dat

Crystal structure of beta-glucosidase from Acetivibrio thermocellus

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