9n3u

Structure of glyoxal oxidase from Fusarium graminearum at 1.28 Angstroms resolution

Method: X-RAY DIFFRACTION D_max: 89.2 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	9n3u
沉积日期 deposition_date	2025-01-31
结构标题 title	Structure of glyoxal oxidase from Fusarium graminearum at 1.28 Angstroms resolution
关键词 keywords	Radical co-factor, Kelch motif, oxidase, 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	26.61 Å
回转半径 Rg (电子) rg_electron	25.65 Å
零角强度 I(0) i0	87749700.00
分子量 molecular_weight	72422.0 kDa
排除体积 excluded_volume	89804 Å³
包络体积 envelope_volume	104400 Å³
水化壳体积 shell_volume	33658 Å³
包络直径 envelope_diameter	92.5 Å
壳层 Rg shell_rg	33.45 Å
包络 Rg envelope_rg	25.99 Å
形状 Rg shape_rg	25.64 Å
总 Rg total_rg	26.42 Å
总原子数 total_atoms	5088
残基数 n_residues	632
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	89.2 Å
Rg (实空间) rg_real	26.58 Å
Rg 误差 (实空间) rg_real_error	0.75 Å
I(0) (实空间) i0_real	8.7750e+07
I(0) 误差 (实空间) i0_real_error	1.3290e+06
Rg (倒空间) rg_reciprocal	26.59 Å
I(0) (倒空间) i0_reciprocal	87750000.0000
解质量估计 total_estimate	0.8772
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	32.7 Å
偏度 Skewness skewness	0.370
峰度 Kurtosis kurtosis	-0.242
角度范围 angular_range	— – 0.3000 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	23120000.0000
实空间数据点数 n_real_points	61
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.805; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.995

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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 (9)

Entity 1 polymer

描述 description	Chromosome 3, complete genome
分子量 formula_weight	72516.8 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	5813

VAKKDGLPGDWEYKGCVFDNNNPYLLQWLYEDAGSYATSNMTIETCLNRCQKFGYSAGGVEYGRQCVCGDLKAVENRGDVWKDDSFCSMACPGDRNSTCGAGNHINYYEWTGASLNTFHYASGPKAGKYDHFSTSPIIPLISSVGINDKIVFVEKHGTSDDDTEGSFEFDYTTNIYRELALKTDVFCSASFTLPDKAGRIINIGGWSAESVYGIRFFTPDSPQGVDNGTNVWEEDYTQLRLFDPRWYPTALVLSNGSILAMGGESGSDAPIVPTAEVLPHPAGVTESTYVDYLERAENIGRTNSYPHMAILPSGNIFFTQFNESRLLSQVDFQSIKKLPDMPGQINNPLTGRNYPLQGTLMVLPHKAPYSDPVEILICGGTTHEPGNDALDNCVLMAPDVEGAEWAIERMPSKRVMPNMVALPDGRYLILGGAQVGRGGFGLADNANLNAVMYDPEEPLGQRMTVLANTTIARLYHSEAVLLSDGKVLVSGSDPQDQGKHPQEKRIEYFWPDYLLSGATQPNFTISDRDWTYGESYTFTLTSDLEEGASKLRVSLMASVGATHGVSMGQRTLFPEFSCSGKTCSVTAPPNAFVSPPSWYQMFVLDGPTPSHAIWVRIGGDPGKLGDWPKLPGFTPPGVALEQKLISEEDLNSAVDHHHHHH

来源 Source

来源生物 organism	Fusarium graminearum PH-1
NCBI 分类编号 ncbi_taxonomy_id	229533
宿主生物 host_organism	Komagataella pastoris

Entity 2 branched

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

Entity 3 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	1

Entity 4 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	1

Entity 5 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	1

Entity 6 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	1

Entity 7 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 8 non-polymer

描述 description	SODIUM ION
分子量 formula_weight	23.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 9 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	592

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7. 引用文献 (1)

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晶胞边长 a length_a	86.000 Å
晶胞边长 b length_b	129.980 Å
晶胞边长 c length_c	134.050 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	8

空间群 space_group	C 2 2 21
空间群编号 int_tables_number	20
晶系 crystal_system	orthorhombic

分辨率 resolution	1.280 Å
最低分辨率 resolution_low	46.660 Å
R 因子 r_factor	0.1401
R_work r_work	0.1398
R_free r_free	0.1680

fit	/app/data/saxs_computation/n3/9n3u/9n3u.fit
pddf	/app/data/pr_computation/n3/9n3u/9n3u.pr.out
profile	/app/data/saxs_computation/n3/9n3u/9n3u.dat