8yhm

The structure of SdnG covalently binding with the cope rearrangement product

Method: X-RAY DIFFRACTION D_max: 59.9 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	8yhm
沉积日期 deposition_date	2024-02-28
最后修订 last_revision	2025-10-22
结构标题 title	The structure of SdnG covalently binding with the cope rearrangement product
关键词 keywords	Diels Alderase, Norbornene, Sordarin, cope rearrangement, BIOSYNTHETIC PROTEIN; BIOSYNTHETIC PROTEIN
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	19.98 Å
回转半径 Rg (电子) rg_electron	18.97 Å
零角强度 I(0) i0	29703900.00
分子量 molecular_weight	28209.0 kDa
排除体积 excluded_volume	27388 Å³
包络体积 envelope_volume	44441 Å³
水化壳体积 shell_volume	19616 Å³
包络直径 envelope_diameter	60.6 Å
壳层 Rg shell_rg	25.37 Å
包络 Rg envelope_rg	19.16 Å
形状 Rg shape_rg	18.92 Å
总 Rg total_rg	19.72 Å
总原子数 total_atoms	2140
残基数 n_residues	264
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	59.9 Å
Rg (实空间) rg_real	19.87 Å
Rg 误差 (实空间) rg_real_error	0.25 Å
I(0) (实空间) i0_real	2.9700e+07
I(0) 误差 (实空间) i0_real_error	3.5340e+05
Rg (倒空间) rg_reciprocal	19.89 Å
I(0) (倒空间) i0_reciprocal	29700000.0000
解质量估计 total_estimate	0.9137
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	23.6 Å
偏度 Skewness skewness	0.195
峰度 Kurtosis kurtosis	-0.513
角度范围 angular_range	— – 0.4000 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	4790000.0000
实空间数据点数 n_real_points	72
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.961; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.993

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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 (4)

Entity 1 polymer

描述 description	Sordarin/hypoxysordarin biosynthesis cluster protein G
分子量 formula_weight	16213.3 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	2439

MAGKEIQTPDQAEAFVAKVFDVLDSYDYTRFGEVLSTDLKYEGGLQKTSGLDNFINDIKASTQRMPGLQTSHSRYRTELTAEGTIYSEGHSNASLESNPGKVVTVPMIGVFKLDSEDGKIKEMRIYKDRLPFLALHQALPGMKANN

来源 Source

来源生物 organism	Sordaria araneosa
NCBI 分类编号 ncbi_taxonomy_id	573841
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 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	2

Entity 3 non-polymer

描述 description	;(3aR,5R,5aR,8R,8aR,9aR)-5-methanoyl-8,9a-dimethyl-2-propan-2-yl-3,3a,4,5,5a,6,7,8,8a,9-decahydrocyclopenta[g]azulene-1-carboxylic acid ;
分子量 formula_weight	318.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 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	208

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7. 引用文献 (1)

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晶胞边长 a length_a	44.830 Å
晶胞边长 b length_b	59.310 Å
晶胞边长 c length_c	107.740 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	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	orthorhombic

分辨率 resolution	1.720 Å
最低分辨率 resolution_low	39.880 Å
R 因子 r_factor	0.1914
R_work r_work	0.1902
R_free r_free	0.2158

fit	/app/data/saxs_computation/yh/8yhm/8yhm.fit
pddf	/app/data/pr_computation/yh/8yhm/8yhm.pr.out
profile	/app/data/saxs_computation/yh/8yhm/8yhm.dat

The structure of SdnG covalently binding with the cope rearrangement product

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