8oye

Clostridium perfringens chitinase CP4_3455 E196Q with chitin

Method: X-RAY DIFFRACTION D_max: 90.1 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	8oye
沉积日期 deposition_date	2023-05-04
结构标题 title	Clostridium perfringens chitinase CP4_3455 E196Q with chitin
关键词 keywords	chitinase, TIM, substrate, necrotic enteritis, 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	25.82 Å
回转半径 Rg (电子) rg_electron	24.75 Å
零角强度 I(0) i0	68131400.00
分子量 molecular_weight	64432.0 kDa
排除体积 excluded_volume	80358 Å³
包络体积 envelope_volume	93945 Å³
水化壳体积 shell_volume	31434 Å³
包络直径 envelope_diameter	90.8 Å
壳层 Rg shell_rg	32.33 Å
包络 Rg envelope_rg	25.18 Å
形状 Rg shape_rg	24.75 Å
总 Rg total_rg	25.52 Å
总原子数 total_atoms	8868
残基数 n_residues	563
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	90.1 Å
Rg (实空间) rg_real	25.80 Å
Rg 误差 (实空间) rg_real_error	0.75 Å
I(0) (实空间) i0_real	6.8130e+07
I(0) 误差 (实空间) i0_real_error	1.0210e+06
Rg (倒空间) rg_reciprocal	25.81 Å
I(0) (倒空间) i0_reciprocal	68130000.0000
解质量估计 total_estimate	0.8544
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	32.5 Å
偏度 Skewness skewness	0.411
峰度 Kurtosis kurtosis	-0.032
角度范围 angular_range	— – 0.3050 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	19520000.0000
实空间数据点数 n_real_points	62
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.708; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.994

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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	Chitodextrinase
分子量 formula_weight	65171.5 kDa
突变 mutation	E196Q active site mutant
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	9822

MGSSELNRKLVGYFPEWAYSSEAQGYFNVTDLQWDSLTHIQYSFAMVDPSTNKITLSNKHAAIEEDFSEFDLNYNGKKIELDPSLPYKGHFNVLQTMKKNYPDVSLLISVGGWTGTRCFYTMIDTDNRINTFADSCVDFIRKYGFDGVDIDFQYPSSTSQSGNPDDFDLSEPRRTKLNERYNILIKTLREKIDMASKEDGKEYLLTAAVTASPWVLGGISDNTYAKYLDFLSIMSYDYHGGWNEYVEHLAGIYPNKEDRETVTQIMPTLCMDWAYRYYRGVLPAEKILMGIPYYTRGWENVQGGINGLHGSSKTPASGKYNILGDDLNNDGVLEPAGANPLWHVLNLMEQDPNLKVYWDEISKVPYVWQNDKKVFVSFENEKSIDARLEYIQNKNLGGALIWVMNGDYGLNPNYVEGSNKINEGKYTFGDTLTKRLSQGLKKMGVCNKTPDDLNISLEPINVDVKFNGKYDHPNYTYSIDITNYTDKEIKGGWNVSFDLPKSAVFKSSWGGTYSVTDNGDFNTITLTSGAWQNIAPNSTITVQGMIGLCFSGIRNVTFNGMNPIGNDKSHHHHHH

来源 Source

来源生物 organism	Clostridium perfringens
NCBI 分类编号 ncbi_taxonomy_id	1502
宿主生物 host_organism	Escherichia coli

Entity 2 branched

描述 description	;2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	1034.0 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 3 non-polymer

描述 description	DIMETHYL SULFOXIDE
分子量 formula_weight	78.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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	576

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6. 折叠分类 (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

结构域编号 domain_id	8oyeA01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	290 —

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7. 引用文献 (1)

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晶胞边长 a length_a	50.486 Å
晶胞边长 b length_b	111.599 Å
晶胞边长 c length_c	108.916 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	1.350 Å
最低分辨率 resolution_low	77.950 Å
R 因子 r_factor	0.1474
R_work r_work	0.1472
R_free r_free	0.1612

fit	/app/data/saxs_computation/oy/8oye/8oye.fit
pddf	/app/data/pr_computation/oy/8oye/8oye.pr.out
profile	/app/data/saxs_computation/oy/8oye/8oye.dat