1xc6

Native Structure Of Beta-Galactosidase from Penicillium sp. in complex with Galactose

Method: X-RAY DIFFRACTION D_max: 109.2 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	1xc6
沉积日期 deposition_date	2004-09-01
结构标题 title	Native Structure Of Beta-Galactosidase from Penicillium sp. in complex with Galactose
关键词 keywords	Tim Barrel Domain, Glycoside Hydrolase, Family GH35, Glycoprotein, Penicillium, Quick Cryo Soaking, 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	31.52 Å
回转半径 Rg (电子) rg_electron	30.55 Å
零角强度 I(0) i0	259768000.00
分子量 molecular_weight	118220.0 kDa
排除体积 excluded_volume	141130 Å³
包络体积 envelope_volume	164650 Å³
水化壳体积 shell_volume	44320 Å³
包络直径 envelope_diameter	114.9 Å
壳层 Rg shell_rg	38.18 Å
包络 Rg envelope_rg	30.75 Å
形状 Rg shape_rg	30.37 Å
总 Rg total_rg	31.59 Å
总原子数 total_atoms	7942
残基数 n_residues	971
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	109.2 Å
Rg (实空间) rg_real	31.52 Å
Rg 误差 (实空间) rg_real_error	0.76 Å
I(0) (实空间) i0_real	2.5980e+08
I(0) 误差 (实空间) i0_real_error	3.7860e+06
Rg (倒空间) rg_reciprocal	31.52 Å
I(0) (倒空间) i0_reciprocal	259800000.0000
解质量估计 total_estimate	0.8608
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	34.9 Å
偏度 Skewness skewness	0.427
峰度 Kurtosis kurtosis	-0.142
角度范围 angular_range	— – 0.2500 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	56490000.0000
实空间数据点数 n_real_points	51
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.744; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.956

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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 (13)

Entity 1 polymer

描述 description	Beta-Galactosidase
分子量 formula_weight	105683.8 kDa
EC 编号 ec_number	3.2.1.23
来源方法 src_method	nat
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	8894

LLQKYVTWDEHSIFVNGERLMIFSGEVHPYRLPVASLYIDIFEKVKALGFNCVSFYVDWALLEGNPGHYSAEGIFDLQPFFDAAKEAGIYLLARPGPYINAEVSGGGFPGWLQRVDGILRTSDEAYLKATDNYASNIAATIAKAQITNGGPIILYQPENEYSGACCGYNGFPDGSYMQYIEDHARDAGIVVPFISNDAWAAGHNAPGTGAGAVDIYGHDSYPLGFDCANPSTWPSGNLPTYFHTSHEQQSPSTPYSLVEFQGGAFDPWGGVGFAKCAALLNHEFERVFYKNDFSFGVAFLNLYMIFGGTNWGNLGHPGGYTSYDYGSAISESRNITREKYSELKLLGNFAKVSPGYLVANPGDLSTSTYTNTADLTVTPLLGSNSSASSFFVIRHSDYSSQASVEYKLTVPTSAGNLTIPQLGGSLTLSGRDSKIHVTDYDVAGTNILYSTAEVFTWKKFNNEKVLVLYGGPGEHHEFAVSGASSSSVVEGSSSGISSKKVGKALVVAWDVSTARRIVQVGSLKVFLLDRNSAYNYWVPQVPTKGTAPGYSNQETTASSIIVKAGYLVRSAYLDGNDLHIQADFNATTPIEVVGAPSGAKNLVINGKKTQTKVDKNGIWSASVAYTAPKVQLPSLKSLKWKSVDTLPEAKNTYDDSAWTSADHAYTNNSAHSLQTPTSLFASDYGYHTGALLFRGHFTANGKEKTFFVQTKGGTAYGHSIWINETYVGSWAGTSINDNNNATYTLPTLQSGKNYVITVVIDNMGLDEDWTIGSEDMKNPRGIIQYSLSGQEASAISWKLTGNLGGENYRDTVRGPLNEGGLYAERQGFHQPQPPTQKWDSSSPFTGLTKPGIRFYSTSFDLDLPSGYDIPLYFNFGNSTSTPAAYRVQLYVNGYQYGKYVNNIGPQTSFPVPEGILNYHGTNWLALSLWAQEDNGAKLDSFELINTTPVLTSLGEVKSVNQPKYQARKGAY

Entity 2 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 3 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)-[beta-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 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	1

Entity 5 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	1

Entity 6 branched

描述 description	;alpha-D-mannopyranose-(1-3)-[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	1235.1 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 7 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	2

Entity 8 non-polymer

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

Entity 9 non-polymer

描述 description	SODIUM ION
分子量 formula_weight	23.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 10 non-polymer

描述 description	PHOSPHATE ION
分子量 formula_weight	95.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 11 non-polymer

描述 description	IODIDE ION
分子量 formula_weight	126.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	52

Entity 12 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	11

Entity 13 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	952

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6. 折叠分类 (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

结构域编号 domain_id	d1xc6a1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.149 — Beta-galactosidase LacA, domain 3
超家族 Superfamily superfamily	b.149.1 — Beta-galactosidase LacA, domain 3
家族 Family family	b.149.1.1 — Beta-galactosidase LacA, domain 3

结构域编号 domain_id	d1xc6a2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.18 — Galactose-binding domain-like
超家族 Superfamily superfamily	b.18.1 — Galactose-binding domain-like
家族 Family family	b.18.1.27 — Beta-galactosidase LacA, domains 4 and 5

结构域编号 domain_id	d1xc6a3
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.18 — Galactose-binding domain-like
超家族 Superfamily superfamily	b.18.1 — Galactose-binding domain-like
家族 Family family	b.18.1.27 — Beta-galactosidase LacA, domains 4 and 5

结构域编号 domain_id	d1xc6a4
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.71 — Glycosyl hydrolase domain
超家族 Superfamily superfamily	b.71.1 — Glycosyl hydrolase domain
家族 Family family	b.71.1.5 — Beta-galactosidase LacA, domain 2

结构域编号 domain_id	d1xc6a5
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.8 — (Trans)glycosidases
家族 Family family	c.1.8.14 — Glycosyl hydrolases family 35 catalytic domain

CATH v4.4 (5 domains)

结构域编号 domain_id	1xc6A01
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	1xc6A02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	102 — 3-layer Sandwich
拓扑 Topology topology	20 — beta-galactosidase, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Beta-galactosidase, domain 2

结构域编号 domain_id	1xc6A03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	390 — beta-galactosidase, domain 3
同源超家族 H-superfamily homologous superfamily	10 — Beta-galactosidase, domain 3

结构域编号 domain_id	1xc6A04
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	260 — Galactose-binding domain-like

结构域编号 domain_id	1xc6A05
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	260 — Galactose-binding domain-like

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7. 引用文献 (2)

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晶胞边长 a length_a	110.960 Å
晶胞边长 b length_b	110.960 Å
晶胞边长 c length_c	161.050 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 43
空间群编号 int_tables_number	78
晶系 crystal_system	—

分辨率 resolution	2.100 Å
最低分辨率 resolution_low	23.400 Å
R 因子 r_factor	—
R_work r_work	0.1709
R_free r_free	0.1859

fit	/app/data/saxs_computation/xc/1xc6/1xc6.fit
pddf	/app/data/pr_computation/xc/1xc6/1xc6.pr.out
profile	/app/data/saxs_computation/xc/1xc6/1xc6.dat