1ukc

Crystal Structure of Aspergillus niger EstA

Method: X-RAY DIFFRACTION D_max: 118.8 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	1ukc
沉积日期 deposition_date	2003-08-19
结构标题 title	Crystal Structure of Aspergillus niger EstA
关键词 keywords	esterase, fungi, a/b hydrolase fold, acetylcholinesterase, 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	35.77 Å
回转半径 Rg (电子) rg_electron	35.45 Å
零角强度 I(0) i0	216266000.00
分子量 molecular_weight	116560.0 kDa
排除体积 excluded_volume	144570 Å³
包络体积 envelope_volume	178930 Å³
水化壳体积 shell_volume	43669 Å³
包络直径 envelope_diameter	129.9 Å
壳层 Rg shell_rg	40.05 Å
包络 Rg envelope_rg	35.59 Å
形状 Rg shape_rg	35.38 Å
总 Rg total_rg	35.95 Å
总原子数 total_atoms	8228
残基数 n_residues	1030
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	118.8 Å
Rg (实空间) rg_real	36.02 Å
Rg 误差 (实空间) rg_real_error	1.01 Å
I(0) (实空间) i0_real	2.1630e+08
I(0) 误差 (实空间) i0_real_error	3.6710e+06
Rg (倒空间) rg_reciprocal	35.86 Å
I(0) (倒空间) i0_reciprocal	216200000.0000
解质量估计 total_estimate	0.8398
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	35.1 Å
偏度 Skewness skewness	0.517
峰度 Kurtosis kurtosis	-0.373
角度范围 angular_range	— – 0.2200 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	53130000.0000
实空间数据点数 n_real_points	45
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.786; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.887; Smooth: 0.667

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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 (9)

Entity 1 polymer

描述 description	EstA
分子量 formula_weight	56932.7 kDa
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	9377

LPTQASHNAQPVINLGYARYQGVRLEAGVDEFLGMRYASPPIGDLRFRAPQDPPANQTLQSATEYGPICIGLDEEESPGDISEDCLFINVFKPSTATSQSKLPVWLFIQGGGYAENSNANYNGTQVIQASDDVIVFVTFNYRVGALGFLASEKVRQNGDLNAGLLDQRKALRWVKQYIEQFGGDPDHIVIHGVSAGAGSVAYHLSAYGGKDEGLFIGAIVESSFWPTQRTVSEMEFQFERFVNDTGCSSARDSLECLREQDIATIQKGNTGSPFPGGSSSPLPDWYFLPVTDGSLVPDELYNAFDAGNFIKVPVLVGDDTDEGSNFAYNASSSADVSRFFKNNYPNLTSQQLNEINQVYPRGKLLPRHAAYFGASSAAYGDATFTCPGNHVASSAARYLPNSVWNYRVNIIDESNIAGGIGVPHTFELPAIFGAGSTGTLSSDSSYLTYNAAIIPVTMHYFISFVQTLNPNTYRYATAPEWNTWGNGQRLRLQTNDTAMEAVPESSLQDCAFWKSLTVPMEV

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-(1-4)-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 3 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	1

Entity 4 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	10

Entity 5 non-polymer

描述 description	alpha-D-mannopyranose
分子量 formula_weight	180.2 kDa
来源方法 src_method	man
拷贝数 entity_count	5

Entity 6 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	2

Entity 7 non-polymer

描述 description	CHLORIDE ION
分子量 formula_weight	35.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 8 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	4

Entity 9 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	1149

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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	d1ukca_
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	d1ukcb_
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	1ukcA00
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	1ukcB00
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	167.489 Å
晶胞边长 b length_b	167.489 Å
晶胞边长 c length_c	112.827 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	120.00 °
晶胞分子数 Z z_pdb	12

空间群 space_group	P 63
空间群编号 int_tables_number	173
晶系 crystal_system	—

分辨率 resolution	2.100 Å
最低分辨率 resolution_low	30.000 Å
R 因子 r_factor	0.1578
R_work r_work	0.1575
R_free r_free	0.1841

fit	/app/data/saxs_computation/uk/1ukc/1ukc.fit
pddf	/app/data/pr_computation/uk/1ukc/1ukc.pr.out
profile	/app/data/saxs_computation/uk/1ukc/1ukc.dat