SAXSdb — 8in1

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8in1
沉积日期 deposition_date	2023-03-08
结构标题 title	beta-glucosidase protein from Aplysia kurodai
关键词 keywords	glucosidase, 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	41.26 Å
回转半径 Rg (电子) rg_electron	40.60 Å
零角强度 I(0) i0	701471000.00
分子量 molecular_weight	218980.0 kDa
排除体积 excluded_volume	273770 Å³
包络体积 envelope_volume	336480 Å³
水化壳体积 shell_volume	67810 Å³
包络直径 envelope_diameter	134.0 Å
壳层 Rg shell_rg	46.88 Å
包络 Rg envelope_rg	40.31 Å
形状 Rg shape_rg	40.56 Å
总 Rg total_rg	41.04 Å
总原子数 total_atoms	15499
残基数 n_residues	1904
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	124.8 Å
Rg (实空间) rg_real	41.06 Å
Rg 误差 (实空间) rg_real_error	0.70 Å
I(0) (实空间) i0_real	7.0150e+08
I(0) 误差 (实空间) i0_real_error	1.1660e+07
Rg (倒空间) rg_reciprocal	41.26 Å
I(0) (倒空间) i0_reciprocal	701600000.0000
解质量估计 total_estimate	0.8999
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	59.1 Å
偏度 Skewness skewness	0.050
峰度 Kurtosis kurtosis	-0.661
角度范围 angular_range	— – 0.1900 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	244400000.0000
实空间数据点数 n_real_points	39
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.956; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.839

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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 (7)

Entity 1 polymer

描述 description	Beta-Glucosidase
分子量 formula_weight	112560.0 kDa
来源方法 src_method	nat
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	15595

MGKVHVILWLPALLGLFVTSARAADLLTDKFPANFTFGVSTSAFPTEGAWDADGKGPSIWDTFTSDSSHVTGGGDAKQSADTYNHVDDDVTLLKDLGVSSYKFSISWPRIFPNGTKESVNQKGVNFYNTLIDKLLANQITPFVSLYYWDLPQDLQDKGGWSKDESVAWFGDYADFCFKTFGNRVKRWVTIDDPFSVAYKGHETGEQAPGVKNVSVTYKVGHNLLLAHAEAYRIYKDNYRTVQKGEVGISLSSEWYVPKTTGVSDVMAARRAMTFRLGWFLEPLVKGDYPLLMQQRVVAARGTANGLPQFSAGDKLKVKDSYDFIGLSHFTSRLVSEDAGVCSGATVGFFCDQGLKMETDLSYPKLEYRPEVNPTSERRLMGFGLLELLKHVTSDYNKPVIYVTENGLSSCGTLQDQNRVEYLREYSNNVLAAIKAGGDVRGFFVWSLLDGFDWSLGYTSKSGLYYVDMGRGERPRFPRSSATFYKKMIANNGLTDELVTYRAYPADRDVFLYDTFPSDFMFGVATSAYQIEGAWNLDGKGPSIWDTFAHNNRLASGQTGDVACDSYHLYMEDVRMLQHLGVNFYRFSIAWSRVMADGTPATTNQAGIDYYNKLIDALLAAGITPVVTLYHWDLPQALENDGGWKNDSVVDQFEAYARLCFEQFGDRVKYWITFNEAFVVSWLGYGIGIFAPGIYDPGTSPYMVAHNIIRSHSRAYHLYSNNFQAKYKGKVGITLDIEWKEPLTDSSEDAAAADRAMQFKLGWFANAIFAGSGDYPQVMRQLVDEKSKRQGLAKSRLPSFTQAEKNLNKGAYDFLALNHYTTNPVNNQPRPNSQPNYEQDQNIDTRYDPCWPDTDASWLKVNPWGIRKLLRWARDHYHNPEIIISESGRPDGEDLTDDGRIYYYKYYINELLKAIKLDGVRVKGYTAWSLMDNLEWTSGYYAKFGLYHVDFNSPNRTRTPRTSATFYQQLIKDRGFPKPASSRRVRRRSRGFHLN

Entity 2 branched

描述 description	;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	878.8 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

Entity 3 branched

描述 description	alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	367.3 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

Entity 4 branched

描述 description	;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	732.7 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

Entity 5 branched

描述 description	alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	570.5 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

Entity 6 non-polymer

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	221.2 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

Entity 7 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	96

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7. 引用文献 (1)

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晶胞边长 a length_a	191.669 Å
晶胞边长 b length_b	191.669 Å
晶胞边长 c length_c	112.551 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 62
空间群编号 int_tables_number	171
晶系 crystal_system	hexagonal

分辨率 resolution	2.700 Å
最低分辨率 resolution_low	49.650 Å
R 因子 r_factor	0.1849
R_work r_work	0.1831
R_free r_free	0.2195

fit	/app/data/saxs_computation/in/8in1/8in1.fit
pddf	/app/data/pr_computation/in/8in1/8in1.pr.out
profile	/app/data/saxs_computation/in/8in1/8in1.dat

beta-glucosidase protein from Aplysia kurodai

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