SAXSdb — 2hl6

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2hl6
沉积日期 deposition_date	2006-07-06
结构标题 title	Structure of homologously expressed Ferrulate esterase of Aspergillus niger in complex with CAPS
关键词 keywords	Esterase, a/b hydrolase fold, glycosylated, CAPS, 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	27.57 Å
回转半径 Rg (电子) rg_electron	26.75 Å
零角强度 I(0) i0	64415300.00
分子量 molecular_weight	59471.0 kDa
排除体积 excluded_volume	72773 Å³
包络体积 envelope_volume	86469 Å³
水化壳体积 shell_volume	27400 Å³
包络直径 envelope_diameter	92.2 Å
壳层 Rg shell_rg	33.51 Å
包络 Rg envelope_rg	26.81 Å
形状 Rg shape_rg	26.74 Å
总 Rg total_rg	27.42 Å
总原子数 total_atoms	4168
残基数 n_residues	520
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	88.9 Å
Rg (实空间) rg_real	27.69 Å
Rg 误差 (实空间) rg_real_error	0.59 Å
I(0) (实空间) i0_real	6.4420e+07
I(0) 误差 (实空间) i0_real_error	1.0100e+06
Rg (倒空间) rg_reciprocal	27.65 Å
I(0) (倒空间) i0_reciprocal	64410000.0000
解质量估计 total_estimate	0.8738
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	26.1 Å
偏度 Skewness skewness	0.385
峰度 Kurtosis kurtosis	-0.595
角度范围 angular_range	— – 0.2900 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	19510000.0000
实空间数据点数 n_real_points	59
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.833; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.938; Smooth: 0.919

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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 (7)

Entity 1 polymer

描述 description	Feruloyl esterase A
分子量 formula_weight	28372.9 kDa
EC 编号 ec_number	3.1.1.73
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	4856

ASTQGISEDLYNRLVEMATISQAAYADLCNIPSTIIKGEKIYNAQTDINGWILRDDTSKEIITVFRGTGSDTNLQLDTNYTLTPFDTLPQCNDCEVHGGYYIGWISVQDQVESLVKQQASQYPDYALTVTGHSLGASMAALTAAQLSATYDNVRLYTFGEPRSGNQAFASYMNDAFQVSSPETTQYFRVTHSNDGIPNLPPAEQGYAHGGVEYWSVDPYSAQNTFVCTGDEVQCCEAQGGQGVNDAHTTYFGMTSGACTW

来源 Source

来源生物 organism	Aspergillus niger
NCBI 分类编号 ncbi_taxonomy_id	5061
宿主生物 host_organism	Aspergillus niger

Entity 2 branched

描述 description	;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	910.8 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 3 branched

描述 description	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	586.5 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 4 non-polymer

描述 description	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 5 non-polymer

描述 description	1,2-ETHANEDIOL
分子量 formula_weight	62.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	8

Entity 6 non-polymer

描述 description	3-CYCLOHEXYL-1-PROPYLSULFONIC ACID
分子量 formula_weight	221.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 7 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	617

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6. 折叠分类 (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d2hl6a_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.69 — alpha/beta-Hydrolases
超家族 Superfamily superfamily	c.69.1 — alpha/beta-Hydrolases
家族 Family family	c.69.1.17 — Fungal lipases

结构域编号 domain_id	d2hl6b_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.69 — alpha/beta-Hydrolases
超家族 Superfamily superfamily	c.69.1 — alpha/beta-Hydrolases
家族 Family family	c.69.1.17 — Fungal lipases

CATH v4.4 (2 domains)

结构域编号 domain_id	2hl6A00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

结构域编号 domain_id	2hl6B00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

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7. 引用文献 (1)

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晶胞边长 a length_a	145.520 Å
晶胞边长 b length_b	51.700 Å
晶胞边长 c length_c	99.588 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	127.98 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	—

分辨率 resolution	1.550 Å
最低分辨率 resolution_low	39.210 Å
R 因子 r_factor	0.1650
R_work r_work	0.1630
R_free r_free	0.1960

fit	/app/data/saxs_computation/hl/2hl6/2hl6.fit
pddf	/app/data/pr_computation/hl/2hl6/2hl6.pr.out
profile	/app/data/saxs_computation/hl/2hl6/2hl6.dat

Structure of homologously expressed Ferrulate esterase of Aspergillus niger in complex with CAPS

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution