9l3o

Crystal structure of endo-processive xyloglucanase Xeg5A from Aspergillus oryzae with XXLG

Method: X-RAY DIFFRACTION D_max: 127.6 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	9l3o
沉积日期 deposition_date	2024-12-19
最后修订 last_revision	2025-06-25
结构标题 title	Crystal structure of endo-processive xyloglucanase Xeg5A from Aspergillus oryzae with XXLG
关键词 keywords	Xyloglucanase, Complex, 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	36.72 Å
回转半径 Rg (电子) rg_electron	36.32 Å
零角强度 I(0) i0	273550000.00
分子量 molecular_weight	133890.0 kDa
排除体积 excluded_volume	167140 Å³
包络体积 envelope_volume	214630 Å³
水化壳体积 shell_volume	49010 Å³
包络直径 envelope_diameter	144.5 Å
壳层 Rg shell_rg	42.49 Å
包络 Rg envelope_rg	36.42 Å
形状 Rg shape_rg	36.27 Å
总 Rg total_rg	36.87 Å
总原子数 total_atoms	9443
残基数 n_residues	1100
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	127.6 Å
Rg (实空间) rg_real	36.78 Å
Rg 误差 (实空间) rg_real_error	1.38 Å
I(0) (实空间) i0_real	2.7350e+08
I(0) 误差 (实空间) i0_real_error	5.1900e+06
Rg (倒空间) rg_reciprocal	36.75 Å
I(0) (倒空间) i0_reciprocal	273500000.0000
解质量估计 total_estimate	0.7935
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	3
主峰位置 r_peak_primary	41.5 Å
偏度 Skewness skewness	0.374
峰度 Kurtosis kurtosis	-0.356
角度范围 angular_range	— – 0.2150 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	100700000.0000
实空间数据点数 n_real_points	44
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.802; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.915; 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 (13)

Entity 1 polymer

描述 description	Glycoside hydrolase superfamily
分子量 formula_weight	71499.8 kDa
来源方法 src_method	man
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	9964

MRFPSIFTAVLFAASSALAAPVNTTTEDETAQIPAEAVIGYSDLEGDFDVAVLPFSNSTNNGLLFINTTIASIAAKEEGVSLEKREAEALSANCTGSFDAISASDFVANINPGWNLGNSLDATPNEDSWNNPTVQESTFDYVKAAGFKSVRLPVTWTHHFTSESPDWTVDPKWLQRVSDVIDMITSRGLYTIVNVHHDSWEWADVTKSDANITQIEQKFEKLWYQIGTKLACKSSMVAFETINEPPCNTAEDGAKINKFNEIFLRAINRAGGFNAKRVVNLVGGGMDSVKTSQWFKTPANITNPWALQFHFYSPYDFIFSAWGKTIWGSDSDKSELDSTLGLLRGNFTDVPIVLGEFDASPTNTEPAARWKYHDYLIRSTKKYNMSPIIWDNGLDHLDRSSGIWRDPVSIEIITNGNETNSLPDSTVDTSAPSQSSSAYIYHKVGTEVTDQTLPFIFNDNTLVSIQDSKGTTLKADTDYTVSGSNITFPASFLSTYYSETSEPGLLPNFTLKFSSGASPVVQLVQWDTPTLSKTSAAASSISGSDLSIPITWKGLPKLATVKALLNNGTYLVDDFTQWFGPFGEARTTYSNQWNWDDKNVILTQATVEAVVAAGQDTVFTFEFFPRVDTTTNTVNFTLTVVDHHHHHH

来源 Source

来源生物 organism	Aspergillus oryzae RIB40
NCBI 分类编号 ncbi_taxonomy_id	510516
宿主生物 host_organism	Komagataella pastoris

Entity 2 branched

描述 description	;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-[alpha-D-mannopyranose-(1-6)]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	1721.5 kDa
来源方法 src_method	man
拷贝数 entity_count	2

Entity 3 branched

描述 description	;alpha-D-mannopyranose-(1-2)-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	1235.1 kDa
来源方法 src_method	man
拷贝数 entity_count	2

Entity 4 branched

描述 description	;alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-[beta-D-galactopyranose-(1-2)-alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-beta-D-glucopyranose ;
分子量 formula_weight	1225.1 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 5 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 6 branched

描述 description	;alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-[beta-D-galactopyranose-(1-2)-alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-beta-D-glucopyranose ;
分子量 formula_weight	1092.9 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 7 non-polymer

描述 description	TETRAETHYLENE GLYCOL
分子量 formula_weight	194.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 8 non-polymer

描述 description	alpha-D-mannopyranose
分子量 formula_weight	180.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 9 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	7

Entity 10 non-polymer

描述 description	beta-D-glucopyranose
分子量 formula_weight	180.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 11 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	3

Entity 12 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	2

Entity 13 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	512

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7. 引用文献 (1)

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晶胞边长 a length_a	79.706 Å
晶胞边长 b length_b	105.896 Å
晶胞边长 c length_c	82.946 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	91.60 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	monoclinic

分辨率 resolution	2.000 Å
最低分辨率 resolution_low	39.840 Å
R 因子 r_factor	0.2059
R_work r_work	0.2037
R_free r_free	0.2479

fit	/app/data/saxs_computation/l3/9l3o/9l3o.fit
pddf	/app/data/pr_computation/l3/9l3o/9l3o.pr.out
profile	/app/data/saxs_computation/l3/9l3o/9l3o.dat