8po9

Polyethylene oxidation hexamerin PEase Cibeles (XP_026756460) from Galleria mellonella

Method: X-RAY DIFFRACTION D_max: 144.1 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	8po9
沉积日期 deposition_date	2023-07-03
结构标题 title	Polyethylene oxidation hexamerin PEase Cibeles (XP_026756460) from Galleria mellonella
关键词 keywords	Polyethylene oxidation enzyme, PEase, XP_026756460, Cibeles, OXIDOREDUCTASE; OXIDOREDUCTASE
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	47.20 Å
回转半径 Rg (电子) rg_electron	46.31 Å
零角强度 I(0) i0	3189260000.00
分子量 molecular_weight	500870.0 kDa
排除体积 excluded_volume	635080 Å³
包络体积 envelope_volume	772040 Å³
水化壳体积 shell_volume	126090 Å³
包络直径 envelope_diameter	144.7 Å
壳层 Rg shell_rg	58.82 Å
包络 Rg envelope_rg	46.16 Å
形状 Rg shape_rg	46.25 Å
总 Rg total_rg	46.89 Å
总原子数 total_atoms	35539
残基数 n_residues	4055
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	144.1 Å
Rg (实空间) rg_real	46.78 Å
Rg 误差 (实空间) rg_real_error	0.49 Å
I(0) (实空间) i0_real	3.1890e+09
I(0) 误差 (实空间) i0_real_error	5.0680e+07
Rg (倒空间) rg_reciprocal	47.20 Å
I(0) (倒空间) i0_reciprocal	3191000000.0000
解质量估计 total_estimate	0.5906
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	61.1 Å
偏度 Skewness skewness	0.054
峰度 Kurtosis kurtosis	-0.551
角度范围 angular_range	— – 0.1650 Å⁻¹
当前正则化参数 α current_alpha	0.0008
最高正则化参数 α highest_alpha	1753000000.0000
实空间数据点数 n_real_points	34
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.905; Stabil: 1.000; Sysdev: 0.006; Positv: 1.000; Valcen: 0.942; Smooth: 0.000

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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 (15)

Entity 1 polymer

描述 description	Arylphorin
分子量 formula_weight	83778.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	6

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F
原子数 atom_count	37172

MQTVLFLAALVSLAAAGYPQYHYDVETRKLDPSLLNIQTKVLSLLENWKQVNPDDEYYKIGKEYNVEANMESYTNREVVTEFLSLYKAGFIPKNEVFSIFYENQALEVIALYRLFYYAKDFETFYKTAAFARVWLNEGQFVYAFYLAVIHRADTRGIVLPAPYEIWPEYFMNSDVLSKIYRIQMQKGLIIPEQGPYYGILSKDNAYYFYANYSGPLTYEDNENLLSYFIEDIGWNSYYYYFHNRFPFWENGEQLIGPLKERRGEIYYYVYQKILARYYLERLANGLGEIPRFNWLDKYQTSYYPLLSSYQLPFAQRNDDYYLASGDNINDIQFIDTYEKTFLQLLQKGQFKAYKQEVDLYNSKSINFVGNYWQSNADLYEKVPKRNYWRSYEATARRVLGAAPRSSINYENMNIPTALDFYQTSLRDPAFYQLYAKILDYINEYKEYLEPYSQDVLHYVGVKINDVKVDKLVTYFEYFDWNATNAVYLSEQQLDTVSPSYIVRQPRLNNKPFTVNIDIKSDVESEVVVKIFLGPKYDGNGLPISLEDNWINFIELDWFTHKLTSGQNKIARKSEEFFFFKDDSVSLFKIYELLSNGQVPSYMVDRYIYLPRRLILPRGTQRGFPLQLFVVVYPYQAPVKEWESMRQYIVDNKPFGYPFDRPVTLPYYFNQPNMYFKDVYVYQEGEQYPYYNSYWSQNQVSNH

Entity 2 branched

描述 description	;alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[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	1073.0 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 3 branched

描述 description	;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	910.8 kDa
来源方法 src_method	man
拷贝数 entity_count	7

Entity 4 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	2

Entity 5 branched

描述 description	;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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	1559.4 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 6 branched

描述 description	;alpha-D-mannopyranose-(1-2)-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 7 non-polymer

描述 description	COPPER (II) ION
分子量 formula_weight	63.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

Entity 8 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	5

Entity 9 non-polymer

描述 description	CHLORIDE ION
分子量 formula_weight	35.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	22

Entity 10 non-polymer

描述 description	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
分子量 formula_weight	195.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 11 non-polymer

描述 description	(4S)-2-METHYL-2,4-PENTANEDIOL
分子量 formula_weight	118.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	11

Entity 12 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	6

Entity 13 non-polymer

描述 description	GLYCINE
分子量 formula_weight	75.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	7

Entity 14 non-polymer

描述 description	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 15 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	1589

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7. 引用文献 (1)

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晶胞边长 a length_a	93.750 Å
晶胞边长 b length_b	196.580 Å
晶胞边长 c length_c	224.120 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	90.00 °
晶胞分子数 Z z_pdb	24

空间群 space_group	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	orthorhombic

分辨率 resolution	2.200 Å
最低分辨率 resolution_low	49.260 Å
R 因子 r_factor	0.1737
R_work r_work	0.1713
R_free r_free	0.2181

fit	/app/data/saxs_computation/po/8po9/8po9.fit
pddf	/app/data/pr_computation/po/8po9/8po9.pr.out
profile	/app/data/saxs_computation/po/8po9/8po9.dat