9hdl

;Crystal structure of Pyrimidine Nucleoside 2'-Hydroxylase (PDN2'H) from Neurospora crassa ;

Method: X-RAY DIFFRACTION D_max: 76.9 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	9hdl
沉积日期 deposition_date	2024-11-12
最后修订 last_revision	2025-02-26
结构标题 title	;Crystal structure of Pyrimidine Nucleoside 2'-Hydroxylase (PDN2'H) from Neurospora crassa ;
关键词 keywords	alpha-ketoglutarate-dependent dioxygenase, nucleoside hydroxylase, 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	21.26 Å
回转半径 Rg (电子) rg_electron	20.00 Å
零角强度 I(0) i0	23823400.00
分子量 molecular_weight	37445.0 kDa
排除体积 excluded_volume	46948 Å³
包络体积 envelope_volume	54865 Å³
水化壳体积 shell_volume	22520 Å³
包络直径 envelope_diameter	75.6 Å
壳层 Rg shell_rg	26.99 Å
包络 Rg envelope_rg	20.41 Å
形状 Rg shape_rg	19.99 Å
总 Rg total_rg	20.95 Å
总原子数 total_atoms	2635
残基数 n_residues	344
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	76.9 Å
Rg (实空间) rg_real	22.09 Å
Rg 误差 (实空间) rg_real_error	0.28 Å
I(0) (实空间) i0_real	2.3850e+07
I(0) 误差 (实空间) i0_real_error	2.8790e+05
Rg (倒空间) rg_reciprocal	21.17 Å
I(0) (倒空间) i0_reciprocal	23820000.0000
解质量估计 total_estimate	0.6452
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	26.0 Å
偏度 Skewness skewness	0.508
峰度 Kurtosis kurtosis	0.325
角度范围 angular_range	— – 0.3750 Å⁻¹
当前正则化参数 α current_alpha	4.3910
最高正则化参数 α highest_alpha	7026000.0000
实空间数据点数 n_real_points	69
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.715; Stabil: 0.893; Sysdev: 0.000; Positv: 1.000; Valcen: 0.972; Smooth: 0.644

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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 (3)

Entity 1 polymer

描述 description	Clavaminate synthase-like protein
分子量 formula_weight	42508.7 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	2845

MGSSHHHHHHSSGLVPRGSHMAPIAQAVTVSLNDLKNGTVSLEALEEAFGPDSLGILVVKDVPAEFAELRHRLLSYSSYLGNLPKSELDRLENEKAKYLTGWSLGKETLKNGQVDNLKGSYYANCAFYVDPSLSCAKPTEEFNPDNFPEYLSPNLWPQESTLPGFKPTFEDLCRLIIDVAVLVARACDRFAEKQIAGYPAGYLEGVVKTSTTTKARLLHYFPEEATATDASKESNKEEEGDEDDWCATHLDHGCLTGLTSAMFVDEAATPPVVNPSVNGSLPPLGELPTSPDPKAGLYIKSRTGQTVQVKIPRDCIAFQTGEALERITGGKFKAVPHFVRGARAEMSAGRIARNTLAVFTQPNLGDEVDMEQHITFGEFARGIVAKNTVS

来源 Source

来源生物 organism	Neurospora crassa
NCBI 分类编号 ncbi_taxonomy_id	5141
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	FE (III) ION
分子量 formula_weight	55.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 3 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	192

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7. 引用文献 (1)

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晶胞边长 a length_a	58.105 Å
晶胞边长 b length_b	61.744 Å
晶胞边长 c length_c	84.325 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	4

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

分辨率 resolution	1.600 Å
最低分辨率 resolution_low	49.820 Å
R 因子 r_factor	0.1830
R_work r_work	0.1814
R_free r_free	0.2132

fit	/app/data/saxs_computation/hd/9hdl/9hdl.fit
pddf	/app/data/pr_computation/hd/9hdl/9hdl.pr.out
profile	/app/data/saxs_computation/hd/9hdl/9hdl.dat

;Crystal structure of Pyrimidine Nucleoside 2'-Hydroxylase (PDN2'H) from Neurospora crassa ;

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

1. 结构基本信息 1. Structure Basics

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

4. 晶体学与实验 4. Crystallography & Experiment

晶胞参数 Unit Cell

对称性 Symmetry

精修参数 Refinement

衍射实验 Diffraction