8ymy

;X-Ray crystal structure of glycoside hydrolase family 6 cellobiohydrolase from Phanerochaete chrysosporium PcCel6A C240S/R347K/C393S cocrystallized with cellotriose ;

Method: X-RAY DIFFRACTION D_max: 61.0 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	8ymy
沉积日期 deposition_date	2024-03-10
最后修订 last_revision	2025-03-12
结构标题 title	;X-Ray crystal structure of glycoside hydrolase family 6 cellobiohydrolase from Phanerochaete chrysosporium PcCel6A C240S/R347K/C393S cocrystallized with cellotriose ;
关键词 keywords	Glycoside hydrolase family 6, cellobiohydrolase, cellulase, catalytic domain, mutant, 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	20.19 Å
回转半径 Rg (电子) rg_electron	19.00 Å
零角强度 I(0) i0	26233900.00
分子量 molecular_weight	39161.0 kDa
排除体积 excluded_volume	48856 Å³
包络体积 envelope_volume	53644 Å³
水化壳体积 shell_volume	22789 Å³
包络直径 envelope_diameter	61.9 Å
壳层 Rg shell_rg	26.25 Å
包络 Rg envelope_rg	19.28 Å
形状 Rg shape_rg	18.97 Å
总 Rg total_rg	19.99 Å
总原子数 total_atoms	2766
残基数 n_residues	358
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	61.0 Å
Rg (实空间) rg_real	20.03 Å
Rg 误差 (实空间) rg_real_error	0.22 Å
I(0) (实空间) i0_real	2.6230e+07
I(0) 误差 (实空间) i0_real_error	3.2240e+05
Rg (倒空间) rg_reciprocal	20.06 Å
I(0) (倒空间) i0_reciprocal	26230000.0000
解质量估计 total_estimate	0.9004
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	27.0 Å
偏度 Skewness skewness	0.061
峰度 Kurtosis kurtosis	-0.472
角度范围 angular_range	— – 0.3950 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	6404000.0000
实空间数据点数 n_real_points	71
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.916; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.972; Smooth: 0.981

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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 (5)

Entity 1 polymer

描述 description	Glucanase
分子量 formula_weight	38321.4 kDa
EC 编号 ec_number	3.2.1.-
突变 mutation	C240S, R347K, C393S
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	4290

SANNPWTGFQIFLSPYYANEVAAAAKQITDPTLSSKAASVANIPTFTWLDSVAKIPDLGTYLASASALGKSTGTKQLVQIVIYDLPDRDCAAKASNGEFSIANNGQANYENYIDQIVAQIQQFPDVRVVAVIEPDSLANLVTNLNVQKCANAKTTYLASVNYALTNLAKVGVYMYMDAGHAGWLGWPANLSPAAQLFTQVWQNAGKSPFIKGLATNVANYNALQAASPDPITQGNPNYDEIHYINALAPLLQQAGWDATFIVDQGKSGVQNIRQQWGDWCNIKGAGFGTRPTTNTGSQFIDSIVWVKPGGESDGTSNSSSPRYDSTCSLPDAAQPAPEAGTWFQAYFQTLVSAANPPL

来源 Source

来源生物 organism	Phanerodontia chrysosporium
NCBI 分类编号 ncbi_taxonomy_id	2822231
宿主生物 host_organism	Komagataella pastoris

Entity 2 branched

描述 description	beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose
分子量 formula_weight	342.3 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 3 branched

描述 description	beta-D-glucopyranose-(1-4)-beta-D-glucopyranose
分子量 formula_weight	342.3 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 4 non-polymer

描述 description	beta-D-glucopyranose
分子量 formula_weight	180.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 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	520

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7. 引用文献 (1)

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晶胞边长 a length_a	54.427 Å
晶胞边长 b length_b	67.405 Å
晶胞边长 c length_c	86.435 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	orthorhombic

分辨率 resolution	1.010 Å
最低分辨率 resolution_low	46.060 Å
R 因子 r_factor	0.1624
R_work r_work	0.1622
R_free r_free	0.1768

fit	/app/data/saxs_computation/ym/8ymy/8ymy.fit
pddf	/app/data/pr_computation/ym/8ymy/8ymy.pr.out
profile	/app/data/saxs_computation/ym/8ymy/8ymy.dat

;X-Ray crystal structure of glycoside hydrolase family 6 cellobiohydrolase from Phanerochaete chrysosporium PcCel6A C240S/R347K/C393S cocrystallized with cellotriose ;

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