8iwf

Aspergillus niger Rha-2 and pNPR

Method: X-RAY DIFFRACTION D_max: 88.3 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	8iwf
沉积日期 deposition_date	2023-03-29
结构标题 title	Aspergillus niger Rha-2 and pNPR
关键词 keywords	Alpha-L-rhamnosidase, hydrolase, Pichia pastoris, Aspergillus niger, p-Nitrophenyl-alpha-L-rhamnoside; 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	26.73 Å
回转半径 Rg (电子) rg_electron	25.71 Å
零角强度 I(0) i0	91335300.00
分子量 molecular_weight	74199.0 kDa
排除体积 excluded_volume	92347 Å³
包络体积 envelope_volume	108540 Å³
水化壳体积 shell_volume	34491 Å³
包络直径 envelope_diameter	92.2 Å
壳层 Rg shell_rg	33.79 Å
包络 Rg envelope_rg	26.22 Å
形状 Rg shape_rg	25.66 Å
总 Rg total_rg	26.69 Å
总原子数 total_atoms	5229
残基数 n_residues	630
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	88.3 Å
Rg (实空间) rg_real	26.69 Å
Rg 误差 (实空间) rg_real_error	0.46 Å
I(0) (实空间) i0_real	9.1340e+07
I(0) 误差 (实空间) i0_real_error	1.2020e+06
Rg (倒空间) rg_reciprocal	26.71 Å
I(0) (倒空间) i0_reciprocal	91340000.0000
解质量估计 total_estimate	0.8816
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	0
主峰位置 r_peak_primary	— Å
偏度 Skewness skewness	0.369
峰度 Kurtosis kurtosis	-0.218
角度范围 angular_range	— – 0.2950 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	37420000.0000
实空间数据点数 n_real_points	60
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.827; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.984

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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 (10)

Entity 1 polymer

描述 description	Alpha-L-rhamnosidase
分子量 formula_weight	68325.5 kDa
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	5284

VPYEEYILAPSSRDLAPASVRQVNGSVTNAAALTGAGGQATFNGVSSVTYDFGINVAGIVSVDVASASSESAFIGVTFTESSMWISNEACDATQDAGLDTPLWFAVGQGAGVYSVGKKYTRGAFRYMTVVSNTTATVSLNSVKINYTASPIQDLRAYTGYFHSSDELLNRIWYAGAYTLQLCSIDPTTGDALVGLGAITSSETITLPQTDKWWTNYTITNGSSTLTDGAKRDRLVWPGDMSIALESVAVSTEDLYSVRTALESLYALQKADGQLPYAGKPFYDTVSFTYHLHSLVGAASYYQYTGDRAWLTRYWGQYKKGVQWALSGVDSTGLANITASADWLRFGMGAHNIEANAILYYVLNDAISLAQSLNDNAPIRNWTATAARIKTVANELLWDDKNGLYTDNETTTLHPQDGNSWAVKANLTLSANQSAIISESLAARWGPYGAPAPEAGATVSPFIGGFELQAHYQAGQPDRALDLLRLQWGFMLDDPRMTNSTFIEGYSTDGSLVYAPYTNRPRVSHAHGWSTGPTSALTIYTAGLRVTGPAGATWLYKPQPGNLTQVEAGFSTRLGSFASSFSRSGGRYQELSFTTPNGTTGSVELGDVSGQLVSEGGVKVQLVGGKASGLQGGKWRLNV

来源 Source

来源生物 organism	Aspergillus niger
NCBI 分类编号 ncbi_taxonomy_id	5061
宿主生物 host_organism	Komagataella pastoris

Entity 2 branched

描述 description	;alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	748.7 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 3 branched

描述 description	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	586.5 kDa
来源方法 src_method	man
拷贝数 entity_count	4

Entity 4 branched

描述 description	;alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	748.7 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 5 branched

描述 description	;alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	1073.0 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 6 branched

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	424.4 kDa
来源方法 src_method	man
拷贝数 entity_count	2

Entity 7 non-polymer

描述 description	(2S,3R,4R,5R,6S)-2-methyl-6-[4-[oxidanyl(oxidanylidene)-$l^4-azanyl]phenoxy]oxane-3,4,5-triol
分子量 formula_weight	285.2 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 8 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	syn
拷贝数 entity_count	2

Entity 9 non-polymer

描述 description	GLYCEROL
分子量 formula_weight	92.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	8

Entity 10 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	55

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7. 引用文献 (1)

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晶胞边长 a length_a	104.388 Å
晶胞边长 b length_b	104.388 Å
晶胞边长 c length_c	145.334 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 31 2 1
空间群编号 int_tables_number	152
晶系 crystal_system	trigonal

分辨率 resolution	2.860 Å
最低分辨率 resolution_low	56.640 Å
R 因子 r_factor	0.2045
R_work r_work	0.2022
R_free r_free	0.2499

fit	/app/data/saxs_computation/iw/8iwf/8iwf.fit
pddf	/app/data/pr_computation/iw/8iwf/8iwf.pr.out
profile	/app/data/saxs_computation/iw/8iwf/8iwf.dat