9he9

Unspecific peroxygenase from Psathyrella aberdarensis (PabUPO-II) in complex with lauric acid

Method: X-RAY DIFFRACTION D_max: 111.5 Å Quality: EXCELLENT

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	9he9
沉积日期 deposition_date	2024-11-13
结构标题 title	Unspecific peroxygenase from Psathyrella aberdarensis (PabUPO-II) in complex with lauric acid
关键词 keywords	Peroxygenase, peroxidase, complex, lauric acid, 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	34.93 Å
回转半径 Rg (电子) rg_electron	34.43 Å
零角强度 I(0) i0	223986000.00
分子量 molecular_weight	118510.0 kDa
排除体积 excluded_volume	146930 Å³
包络体积 envelope_volume	184530 Å³
水化壳体积 shell_volume	44675 Å³
包络直径 envelope_diameter	112.8 Å
壳层 Rg shell_rg	41.01 Å
包络 Rg envelope_rg	34.07 Å
形状 Rg shape_rg	34.42 Å
总 Rg total_rg	34.91 Å
总原子数 total_atoms	8365
残基数 n_residues	1005
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	111.5 Å
Rg (实空间) rg_real	34.85 Å
Rg 误差 (实空间) rg_real_error	0.90 Å
I(0) (实空间) i0_real	2.2400e+08
I(0) 误差 (实空间) i0_real_error	3.7900e+06
Rg (倒空间) rg_reciprocal	34.90 Å
I(0) (倒空间) i0_reciprocal	224000000.0000
解质量估计 total_estimate	0.9005
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	37.1 Å
偏度 Skewness skewness	0.174
峰度 Kurtosis kurtosis	-0.641
角度范围 angular_range	— – 0.2250 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	42380000.0000
实空间数据点数 n_real_points	46
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.933; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.905

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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	Heme-thiolate peroxidase
分子量 formula_weight	36630.4 kDa
EC 编号 ec_number	1.11.2.1
来源方法 src_method	man
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C
原子数 atom_count	9241

QGVDPPPPPGPPSFTGTKLVNDADHPWQPLREGDIRGPCPGLNTLASHGYLPRDGVATPAQIITATQEGFNFENNAAIVATYLGHLLNGNLVTDLLSIGGATPKTGPPPPPPAHAGGLNVHGTFEGDAGMTRADEFFGDNHSFNQTLFDKFVDFSNRYGGGFYNLTVAGELRYSRIQDSIATNPEFQFKNVRFITAYGETVFPINLFVDGRVTTDRKLSMEDAASIFRDMRFPDDFHRSAVPASNEGADQVLAAHPWVPGGNADNQVNNYVEDPDSADFTHLCRLYEFVVGSVQELYPNPTGILRRNLIKNLHYWWTGVNVAFGGCDELFPYGQL

来源 Source

来源生物 organism	Candolleomyces aberdarensis
通用名 common_name	basidiomycete fungi
NCBI 分类编号 ncbi_taxonomy_id	2316362
宿主生物 host_organism	Komagataella phaffii CBS 7435

Entity 2 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	1

Entity 3 branched

描述 description	;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	1235.1 kDa
来源方法 src_method	man
拷贝数 entity_count	1

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	2

Entity 5 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 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	1

Entity 7 non-polymer

描述 description	LAURIC ACID
分子量 formula_weight	200.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 8 non-polymer

描述 description	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
分子量 formula_weight	238.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

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	3

Entity 10 non-polymer

描述 description	PROTOPORPHYRIN IX CONTAINING FE
分子量 formula_weight	616.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 11 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	5

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	3

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	738

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7. 引用文献 (1)

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晶胞边长 a length_a	271.878 Å
晶胞边长 b length_b	75.001 Å
晶胞边长 c length_c	105.446 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	111.74 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	12

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	—

分辨率 resolution	2.150 Å
最低分辨率 resolution_low	48.370 Å
R 因子 r_factor	0.2000
R_work r_work	0.1986
R_free r_free	0.2269

fit	/app/data/saxs_computation/he/9he9/9he9.fit
pddf	/app/data/pr_computation/he/9he9/9he9.pr.out
profile	/app/data/saxs_computation/he/9he9/9he9.dat