SAXSdb — 1hjs

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1hjs
沉积日期 deposition_date	2003-02-27
结构标题 title	Structure of two fungal beta-1,4-galactanases: searching for the basis for temperature and pH optimum.
关键词 keywords	BETA-1, 4-GALACTANASES, FAMILY 53 GLYCOSIDE HYDROLASE, THERMOSTABILITY, PH OPTIMUM, CLAN GH-A, THERMOPHILE, ALKALOPHILE, 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	55.34 Å
回转半径 Rg (电子) rg_electron	55.02 Å
零角强度 I(0) i0	332897000.00
分子量 molecular_weight	150730.0 kDa
排除体积 excluded_volume	187530 Å³
包络体积 envelope_volume	282310 Å³
水化壳体积 shell_volume	43676 Å³
包络直径 envelope_diameter	162.0 Å
壳层 Rg shell_rg	58.05 Å
包络 Rg envelope_rg	51.17 Å
形状 Rg shape_rg	55.00 Å
总 Rg total_rg	55.16 Å
总原子数 total_atoms	10633
残基数 n_residues	1328
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	167.3 Å
Rg (实空间) rg_real	55.20 Å
Rg 误差 (实空间) rg_real_error	1.90 Å
I(0) (实空间) i0_real	3.3290e+08
I(0) 误差 (实空间) i0_real_error	7.1460e+06
Rg (倒空间) rg_reciprocal	55.41 Å
I(0) (倒空间) i0_reciprocal	333000000.0000
解质量估计 total_estimate	0.6926
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	3
主峰位置 r_peak_primary	95.6 Å
偏度 Skewness skewness	-0.183
峰度 Kurtosis kurtosis	-1.087
角度范围 angular_range	— – 0.1400 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	6414000.0000
实空间数据点数 n_real_points	29
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.205; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.846; Smooth: 0.540

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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 (6)

Entity 1 polymer

描述 description	BETA-1,4-GALACTANASE
分子量 formula_weight	36841.1 kDa
EC 编号 ec_number	3.2.1.89
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,B,C,D
原子数 atom_count	11296

ALTYRGVDWSSVVVEERAGVSYKNTNGNAQPLENILAANGVNTVRQRVWVNPADGNYNLDYNIAIAKRAKAAGLGVYIDFHYSDTWADPAHQTMPAGWPSDIDNLSWKLYNYTLDAANKLQNAGIQPTIVSIGNEIRAGLLWPTGRTENWANIARLLHSAAWGIKDSSLSPKPKIMIHLDNGWDWGTQNWWYTNVLKQGTLELSDFDMMGVSFYPFYSSSATLSALKSSLDNMAKTWNKEIAVVETNWPISCPNPRYSFPSDVKNIPFSPEGQTTFITNVANIVSSVSRGVGLFYWEPAWIHNANLGSSCADNTMFSQSGQALSSLSVFQRI

来源 Source

来源生物 organism	THIELAVIA HETEROTHALLICA
通用名 common_name	MYCELIOPHTHORA THERMOPHILA
NCBI 分类编号 ncbi_taxonomy_id	78579
宿主生物 host_organism	ASPERGILLUS ORYZAE

Entity 2 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	4

Entity 3 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	11

Entity 4 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	13

Entity 5 non-polymer

描述 description	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
分子量 formula_weight	238.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 6 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	643

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6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1hjsa_
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.1.8.3 — beta-glycanases

结构域编号 domain_id	d1hjsb_
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.1.8.3 — beta-glycanases

结构域编号 domain_id	d1hjsc_
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.1.8.3 — beta-glycanases

结构域编号 domain_id	d1hjsd_
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.1.8.3 — beta-glycanases

CATH v4.4 (4 domains)

结构域编号 domain_id	1hjsA00
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	1hjsB00
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	1hjsC00
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	1hjsD00
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

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7. 引用文献 (1)

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晶胞边长 a length_a	108.375 Å
晶胞边长 b length_b	136.145 Å
晶胞边长 c length_c	111.007 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	119.02 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	16

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	1.870 Å
最低分辨率 resolution_low	19.840 Å
R 因子 r_factor	0.1940
R_work r_work	0.1940
R_free r_free	0.2080

fit	/app/data/saxs_computation/hj/1hjs/1hjs.fit
pddf	/app/data/pr_computation/hj/1hjs/1hjs.pr.out
profile	/app/data/saxs_computation/hj/1hjs/1hjs.dat

Structure of two fungal beta-1,4-galactanases: searching for the basis for temperature and pH optimum.

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution