1urx

Crystallographic structure of beta-agarase A in complex with oligoagarose

Method: X-RAY DIFFRACTION D_max: 59.1 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	1urx
沉积日期 deposition_date	2003-11-12
结构标题 title	Crystallographic structure of beta-agarase A in complex with oligoagarose
关键词 keywords	HYDROLASE, BETA-AGARASE, AGAROSE, GLYCOSIDE HYDROLASE, FAMILY 16, DOUBLE HELIX, TWO BINDING-SITES; 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	18.77 Å
回转半径 Rg (电子) rg_electron	17.55 Å
零角强度 I(0) i0	18520000.00
分子量 molecular_weight	32142.0 kDa
排除体积 excluded_volume	39766 Å³
包络体积 envelope_volume	42873 Å³
水化壳体积 shell_volume	19848 Å³
包络直径 envelope_diameter	61.9 Å
壳层 Rg shell_rg	24.43 Å
包络 Rg envelope_rg	17.84 Å
形状 Rg shape_rg	17.53 Å
总 Rg total_rg	18.50 Å
总原子数 total_atoms	2269
残基数 n_residues	268
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	59.1 Å
Rg (实空间) rg_real	18.63 Å
Rg 误差 (实空间) rg_real_error	0.30 Å
I(0) (实空间) i0_real	1.8520e+07
I(0) 误差 (实空间) i0_real_error	2.2050e+05
Rg (倒空间) rg_reciprocal	18.65 Å
I(0) (倒空间) i0_reciprocal	18520000.0000
解质量估计 total_estimate	0.8127
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	3
主峰位置 r_peak_primary	25.1 Å
偏度 Skewness skewness	0.090
峰度 Kurtosis kurtosis	-0.446
角度范围 angular_range	— – 0.4250 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	7587000.0000
实空间数据点数 n_real_points	74
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.859; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.000

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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 (5)

Entity 1 polymer

描述 description	BETA-AGARASE A
分子量 formula_weight	32135.4 kDa
EC 编号 ec_number	3.2.1.81
突变 mutation	YES
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	2642

MDIAQDWNGIPVPANPGNGMTWQLQDNVSDSFNYTSSEGNRPTAFTSKWKPSYINGWTGPGSTIFNAPQAWTNGSQLAIQAQPAGNGKSYNGIITSKNKIQYPVYMEIKAKIMDQVLANAFWTLTDDETQSIDIMEGYGSDRGGTWFAQRMHLSHHTFIRNPFTDYQPMGDATWYYNGGTPWRSAYHRYGCYWKDPFTLEYYIDGVKVRTVTRAEIDPNNHLGGTGLNQATNIIIDCENQTDWRPAATQEELADDSKNIFWVDWIRVYKPVAVSLEHHHHHH

来源 Source

来源生物 organism	ZOBELLIA GALACTANIVORANS
通用名 common_name	ZOBELLIA GALACTANIVORA, S
NCBI 分类编号 ncbi_taxonomy_id	63186
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 branched

描述 description	;3,6-anhydro-alpha-L-galactopyranose-(1-3)-beta-D-galactopyranose-(1-4)-3,6-anhydro-alpha-L-galactopyranose-(1-3)-alpha-D-galactopyranose ;
分子量 formula_weight	630.5 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 3 branched

描述 description	;3,6-anhydro-alpha-L-galactopyranose-(1-3)-beta-D-galactopyranose-(1-4)-3,6-anhydro-alpha-L-galactopyranose-(1-3)-beta-D-galactopyranose-(1-4)-3,6-anhydro-alpha-L-galactopyranose-(1-3)-beta-D-galactopyranose-(1-4)-3,6-anhydro-alpha-L-galactopyranose ;
分子量 formula_weight	1080.9 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 4 non-polymer

描述 description	CALCIUM ION
分子量 formula_weight	40.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 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	354

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6. 折叠分类 (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

结构域编号 domain_id	d1urxa_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.29 — Concanavalin A-like lectins/glucanases
超家族 Superfamily superfamily	b.29.1 — Concanavalin A-like lectins/glucanases
家族 Family family	b.29.1.2 — Glycosyl hydrolases family 16

CATH v4.4 (1 domains)

结构域编号 domain_id	1urxA00
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	200 —

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7. 引用文献 (1)

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晶胞边长 a length_a	51.380 Å
晶胞边长 b length_b	51.380 Å
晶胞边长 c length_c	205.360 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	6

空间群 space_group	P 32 2 1
空间群编号 int_tables_number	154
晶系 crystal_system	—

分辨率 resolution	1.700 Å
最低分辨率 resolution_low	37.200 Å
R 因子 r_factor	0.1564
R_work r_work	0.1550
R_free r_free	0.1825

fit	/app/data/saxs_computation/ur/1urx/1urx.fit
pddf	/app/data/pr_computation/ur/1urx/1urx.pr.out
profile	/app/data/saxs_computation/ur/1urx/1urx.dat