9dk4

ancestral hydroxynitrile lyase with fifteen substitutions

Method: X-RAY DIFFRACTION D_max: 114.8 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	9dk4
沉积日期 deposition_date	2024-09-07
结构标题 title	ancestral hydroxynitrile lyase with fifteen substitutions
关键词 keywords	engineered protein, esterase, hydroxynitrile lyase, hydrolase fold, LYASE; LYASE
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	34.33 Å
回转半径 Rg (电子) rg_electron	33.73 Å
零角强度 I(0) i0	171187000.00
分子量 molecular_weight	110040.0 kDa
排除体积 excluded_volume	139220 Å³
包络体积 envelope_volume	167660 Å³
水化壳体积 shell_volume	42228 Å³
包络直径 envelope_diameter	119.7 Å
壳层 Rg shell_rg	39.54 Å
包络 Rg envelope_rg	33.42 Å
形状 Rg shape_rg	33.74 Å
总 Rg total_rg	34.11 Å
总原子数 total_atoms	7779
残基数 n_residues	993
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	114.8 Å
Rg (实空间) rg_real	34.32 Å
Rg 误差 (实空间) rg_real_error	0.77 Å
I(0) (实空间) i0_real	1.7120e+08
I(0) 误差 (实空间) i0_real_error	2.3810e+06
Rg (倒空间) rg_reciprocal	34.33 Å
I(0) (倒空间) i0_reciprocal	171200000.0000
解质量估计 total_estimate	0.6768
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	47.4 Å
偏度 Skewness skewness	0.289
峰度 Kurtosis kurtosis	-0.405
角度范围 angular_range	— – 0.2300 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	146300000.0000
实空间数据点数 n_real_points	47
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.853; Stabil: 1.000; Sysdev: 0.122; Positv: 1.000; Valcen: 0.990; Smooth: 0.878

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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	Fifteen-substitution variant of an ancestral hydroxynitrile lyase
分子量 formula_weight	31033.2 kDa
突变 mutation	Ile9Val Thr11Gly Ile12Ala Glu79His Cys81Phe His103Leu N104T K147L L152F Asn156Lys Thr159Gln Lys175Pro Gln180Ile Lys236Met Leu237Pro
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	8041

MATAHFVLVHGACHGAWIWYKLKPLLEAAGHKVTALDLAASGIDPRQIEQINTFDEYSEPLLTFMESLPQGEKVILVGHSFGGLNIALAADKYPEKISAAVFLTALMPDTEHSPSYVVDKFMEVFPDWKDTEFSTYTSNNETITGMLLGFKFMREKLYQNCPIEDYELAKMLTRPGSFFINDLAQRPKFTEEGYGSIKRVYVWTDEDKIFPPEFQLWQIENYKPDKVYRVQGGDHMPQLSKTNELAEILQEVADTYADLLAVAGLEHHHHHH

来源 Source

来源生物 organism	synthetic construct
NCBI 分类编号 ncbi_taxonomy_id	32630
宿主生物 host_organism	Escherichia coli

Entity 2 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	7

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	261

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7. 引用文献 (1)

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晶胞边长 a length_a	67.244 Å
晶胞边长 b length_b	80.385 Å
晶胞边长 c length_c	92.823 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.62 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

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	1.880 Å
最低分辨率 resolution_low	46.410 Å
R 因子 r_factor	0.1875
R_work r_work	0.1864
R_free r_free	0.2273

fit	/app/data/saxs_computation/dk/9dk4/9dk4.fit
pddf	/app/data/pr_computation/dk/9dk4/9dk4.pr.out
profile	/app/data/saxs_computation/dk/9dk4/9dk4.dat

ancestral hydroxynitrile lyase with fifteen substitutions

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