8wv2

;Crystal structure of urethanase from Candida parapsilosis and structure-based Engineering to improve the catalytic activity and stability ;

Method: X-RAY DIFFRACTION D_max: 232.9 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	8wv2
沉积日期 deposition_date	2023-10-22
最后修订 last_revision	2024-10-23
结构标题 title	;Crystal structure of urethanase from Candida parapsilosis and structure-based Engineering to improve the catalytic activity and stability ;
关键词 keywords	urethanase, HYDROLASE; HYDROLASE
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	63.98 Å
回转半径 Rg (电子) rg_electron	64.43 Å
零角强度 I(0) i0	3220930000.00
分子量 molecular_weight	493730.0 kDa
排除体积 excluded_volume	623530 Å³
包络体积 envelope_volume	850340 Å³
水化壳体积 shell_volume	113030 Å³
包络直径 envelope_diameter	227.4 Å
壳层 Rg shell_rg	61.63 Å
包络 Rg envelope_rg	63.21 Å
形状 Rg shape_rg	64.42 Å
总 Rg total_rg	64.39 Å
总原子数 total_atoms	34832
残基数 n_residues	4408
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	232.9 Å
Rg (实空间) rg_real	64.65 Å
Rg 误差 (实空间) rg_real_error	2.26 Å
I(0) (实空间) i0_real	3.2220e+09
I(0) 误差 (实空间) i0_real_error	7.4540e+07
Rg (倒空间) rg_reciprocal	63.48 Å
I(0) (倒空间) i0_reciprocal	3215000000.0000
解质量估计 total_estimate	0.8367
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	65.2 Å
偏度 Skewness skewness	0.490
峰度 Kurtosis kurtosis	-0.354
角度范围 angular_range	— – 0.1250 Å⁻¹
当前正则化参数 α current_alpha	0.0219
最高正则化参数 α highest_alpha	135100000.0000
实空间数据点数 n_real_points	26
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.714; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.973; Smooth: 0.758

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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 (2)

Entity 1 polymer

描述 description	Amidase family protein
分子量 formula_weight	61807.2 kDa
来源方法 src_method	man
拷贝数 entity_count	8

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,E,F,G,H,D
原子数 atom_count	35789

MLTDNWKELAGKAQSTFQKSLKQAIELADFDEGLAKRYGALPSAIGANVEDFGSPAQFPLEEYLKALPKKVLDITEKDPVELLKDLKSRKVTCVEVLKAYTAASIVASKLTNCVQEFLPIEALQYAQKLDADYETKKHLPLYGLPFSIKEMIPFVGRSVTHGSLCYLDRIVDYNADIVNILIANGAYPFVRTTNPQSLMMLECVSFSHGRTVNAYNGMLTSGGSSGGEGALNGMRASPFGLGSDIGGSIRCPAAFNGIYGLRSTLGRIPTADYFSCNRGSESILSVTGPLSRSLDTVNLVMKTVIEAKPWLIDPTLVPLDWKRPENKKFRVGIYVSDHIVNPSPPINRALSMVTEKLKSLGNFEVVTFEPYKPEKVTEILGKLYFEDGARDFRATLQTGEPLLEQTRWAIEGAEDLDMHDQWYWNLQKQAYRKEFLKHWCSYTDNDGNVLDAVIAPVFPNVAAKHETTKYWTYTSQWNLLDYPVLAFPVTKVDESLDQPYKNYKPLNDLDKYFYEQYDSPSSFKNAPANLCLVGLRFTDEKLVEIANILRN

来源 Source

来源生物 organism	Candida parapsilosis
NCBI 分类编号 ncbi_taxonomy_id	5480
宿主生物 host_organism	Escherichia coli

Entity 2 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	957

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7. 引用文献 (1)

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晶胞边长 a length_a	63.420 Å
晶胞边长 b length_b	110.158 Å
晶胞边长 c length_c	180.584 Å
晶胞夹角 α angle_alpha	75.84 °
晶胞夹角 β angle_beta	83.62 °
晶胞夹角 γ angle_gamma	73.95 °
晶胞分子数 Z z_pdb	8

空间群 space_group	P 1
空间群编号 int_tables_number	1
晶系 crystal_system	—

分辨率 resolution	2.660 Å
最低分辨率 resolution_low	48.910 Å
R 因子 r_factor	0.2060
R_work r_work	0.2044
R_free r_free	0.2370

fit	/app/data/saxs_computation/wv/8wv2/8wv2.fit
pddf	/app/data/pr_computation/wv/8wv2/8wv2.pr.out
profile	/app/data/saxs_computation/wv/8wv2/8wv2.dat

;Crystal structure of urethanase from Candida parapsilosis and structure-based Engineering to improve the catalytic activity and stability ;

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

5. 实体与聚合体信息 (2)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 water

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)