8idp

Crystal structure of reducing-end xylose-releasing exoxylanase in GH30 from Talaromyces cellulolyticus

Method: X-RAY DIFFRACTION D_max: 138.9 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

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8idp
沉积日期 deposition_date	2023-02-14
结构标题 title	Crystal structure of reducing-end xylose-releasing exoxylanase in GH30 from Talaromyces cellulolyticus
关键词 keywords	HYDROLASE; HYDROLASE
实验方法 method	X-RAY DIFFRACTION

▼

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	42.05 Å
回转半径 Rg (电子) rg_electron	41.88 Å
零角强度 I(0) i0	694169000.00
分子量 molecular_weight	213160.0 kDa
排除体积 excluded_volume	264170 Å³
包络体积 envelope_volume	323010 Å³
水化壳体积 shell_volume	63102 Å³
包络直径 envelope_diameter	144.7 Å
壳层 Rg shell_rg	47.74 Å
包络 Rg envelope_rg	41.70 Å
形状 Rg shape_rg	41.85 Å
总 Rg total_rg	42.26 Å
总原子数 total_atoms	15009
残基数 n_residues	1783
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

▼

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	138.9 Å
Rg (实空间) rg_real	42.10 Å
Rg 误差 (实空间) rg_real_error	1.16 Å
I(0) (实空间) i0_real	6.9420e+08
I(0) 误差 (实空间) i0_real_error	1.2980e+07
Rg (倒空间) rg_reciprocal	42.05 Å
I(0) (倒空间) i0_reciprocal	694100000.0000
解质量估计 total_estimate	0.8896
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	43.9 Å
偏度 Skewness skewness	0.330
峰度 Kurtosis kurtosis	-0.563
角度范围 angular_range	— – 0.1900 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	135000000.0000
实空间数据点数 n_real_points	39
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.891; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.894

▶

4. 晶体学与实验 4. Crystallography & Experiment

▶

5. 实体与聚合体信息 (12)

Entity 1 polymer

描述 description	Reducing-end xylose-releasing exoxylanase Xyn30A
分子量 formula_weight	51076.5 kDa
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,C,B,D
原子数 atom_count	16663

MRHPIPILAVLGRASAWSYSQTLSANIQVNALQRYQEMIGGGCSGAFGWACQQFPTTGLTPENQEEVTKILFDENIGGLSIVRNDIGSSPGSTILPTCPATPAGPFNYQWDGSDSCQFNLTKTALKYNPELYVYANAWSAPGCMKTVGTENDGGQICGVRGTNCTYDWRQAYADYLVQYVKFYQAEGIDISLLGAWNEPDFNPVTYESMESDGFQAKDFLEILYPTVKKAFPNLDVSCCDATGARQERNILYEVQQAGGEHFFDVATWHNYQSSPERPFNVVGKPNIMTEWADGSGPWNTTWDVSGQLAEGLQWALYMHNAFTNSDTSGYNHWWCAGGGADNVLISITGNSYEVSSRLWAFASYFRFARPGSVRIGATSSVENVYVSAYENKNGTVSIPVINAAHFPYEVTIDLQGLKARKRVSTFLTDNSHNVTLMDQSELHGSVLKATVPPRAVQVFWLE

来源 Source

来源生物 organism	Talaromyces pinophilus
NCBI 分类编号 ncbi_taxonomy_id	128442
宿主生物 host_organism	Talaromyces pinophilus

Entity 2 branched

描述 description	;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	1883.7 kDa
来源方法 src_method	man
拷贝数 entity_count	2

Entity 3 branched

描述 description	;alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	1073.0 kDa
来源方法 src_method	man
拷贝数 entity_count	2

Entity 4 branched

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	424.4 kDa
来源方法 src_method	man
拷贝数 entity_count	4

Entity 5 branched

描述 description	;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	1559.4 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 6 branched

描述 description	;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	910.8 kDa
来源方法 src_method	man
拷贝数 entity_count	2

Entity 7 branched

描述 description	;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	1559.4 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 8 non-polymer

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	221.2 kDa
来源方法 src_method	man
拷贝数 entity_count	7

Entity 9 non-polymer

描述 description	GLYCEROL
分子量 formula_weight	92.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	15

Entity 10 non-polymer

描述 description	TETRAETHYLENE GLYCOL
分子量 formula_weight	194.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 11 non-polymer

描述 description	DI(HYDROXYETHYL)ETHER
分子量 formula_weight	106.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 12 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	1521

▼

6. 折叠分类 (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

结构域编号 domain_id	8idpA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	80 — Glycosidases

结构域编号 domain_id	8idpB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	80 — Glycosidases

结构域编号 domain_id	8idpC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	80 — Glycosidases

结构域编号 domain_id	8idpD01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	80 — Glycosidases

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	138.457 Å
晶胞边长 b length_b	120.072 Å
晶胞边长 c length_c	122.834 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	16

空间群 space_group	P 21 21 2
空间群编号 int_tables_number	18
晶系 crystal_system	—

分辨率 resolution	1.800 Å
最低分辨率 resolution_low	40.940 Å
R 因子 r_factor	0.1666
R_work r_work	0.1651
R_free r_free	0.1948

fit	/app/data/saxs_computation/id/8idp/8idp.fit
pddf	/app/data/pr_computation/id/8idp/8idp.pr.out
profile	/app/data/saxs_computation/id/8idp/8idp.dat