SAXSdb — 1ieq

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1ieq
沉积日期 deposition_date	2001-04-11
结构标题 title	CRYSTAL STRUCTURE OF BARLEY BETA-D-GLUCAN GLUCOHYDROLASE ISOENZYME EXO1
关键词 keywords	2-domain fold, 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	25.33 Å
回转半径 Rg (电子) rg_electron	24.73 Å
零角强度 I(0) i0	72084200.00
分子量 molecular_weight	66802.0 kDa
排除体积 excluded_volume	83675 Å³
包络体积 envelope_volume	93795 Å³
水化壳体积 shell_volume	31302 Å³
包络直径 envelope_diameter	93.0 Å
壳层 Rg shell_rg	32.53 Å
包络 Rg envelope_rg	25.13 Å
形状 Rg shape_rg	24.72 Å
总 Rg total_rg	25.54 Å
总原子数 total_atoms	4691
残基数 n_residues	602
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	86.7 Å
Rg (实空间) rg_real	25.35 Å
Rg 误差 (实空间) rg_real_error	0.46 Å
I(0) (实空间) i0_real	7.2080e+07
I(0) 误差 (实空间) i0_real_error	9.3250e+05
Rg (倒空间) rg_reciprocal	25.34 Å
I(0) (倒空间) i0_reciprocal	72080000.0000
解质量估计 total_estimate	0.8565
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	28.9 Å
偏度 Skewness skewness	0.459
峰度 Kurtosis kurtosis	-0.068
角度范围 angular_range	— – 0.3150 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	20650000.0000
实空间数据点数 n_real_points	64
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.740; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.968; Smooth: 0.942

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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-D-GLUCAN GLUCOHYDROLASE ISOENZYME EXO1
分子量 formula_weight	65475.6 kDa
EC 编号 ec_number	3.2.1.58
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	4911

DYVLYKDATKPVEDRVADLLGRMTLAEKIGQMTQIERLVATPDVLRDNFIGSLLSGGGSVPRKGATAKEWQDMVDGFQKACMSTRLGIPMIYGIDAVHGQNNVYGATIFPHNVGLGATRDPYLVKRIGEATALEVRATGIQYAFAPCIAVCRDPRWGRCYESYSEDRRIVQSMTELIPGLQGDVPKDFTSGMPFVAGKNKVAACAKHFVGDGGTVDGINENNTIINREGLMNIHMPAYKNAMDKGVSTVMISYSSWNGVKMHANQDLVTGYLKDTLKFKGFVISDWEGIDRITTPAGSDYSYSVKASILAGLDMIMVPNKYQQFISILTGHVNGGVIPMSRIDDAVTRILRVKFTMGLFENPYADPAMAEQLGKQEHRDLAREAARKSLVLLKNGKTSTDAPLLPLPKKAPKILVAGSHADNLGYQCGGWTIEWQGDTGRTTVGTTILEAVKAAVDPSTVVVFAENPDAEFVKSGGFSYAIVAVGEHPYTETKGDNLNLTIPEPGLSTVQAVCGGVRCATVLISGRPVVVQPLLAASDALVAAWLPGSEGQGVTDALFGDFGFTGRLPRTWFKSVDQLPMNVGDAHYDPLFRLGYGLTTNATKKY

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	;2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	1098.0 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 4 non-polymer

描述 description	beta-D-glucopyranose
分子量 formula_weight	180.2 kDa
来源方法 src_method	man
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	220

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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	d1ieqa1
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.1.8.7 — NagZ-like

结构域编号 domain_id	d1ieqa2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.23 — Flavodoxin-like
超家族 Superfamily superfamily	c.23.11 — Beta-D-glucan exohydrolase, C-terminal domain-like
家族 Family family	c.23.11.1 — Beta-D-glucan exohydrolase, C-terminal domain-like

CATH v4.4 (2 domains)

结构域编号 domain_id	1ieqA01
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	300 — Glycoside hydrolase, family 3, N-terminal domain

结构域编号 domain_id	1ieqA02
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	1700 — Glycoside hydrolase family 3 C-terminal domain

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7. 引用文献 (1)

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晶胞边长 a length_a	100.951 Å
晶胞边长 b length_b	100.951 Å
晶胞边长 c length_c	181.196 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	8

空间群 space_group	P 43 21 2
空间群编号 int_tables_number	96
晶系 crystal_system	—

分辨率 resolution	2.700 Å
最低分辨率 resolution_low	15.000 Å
R 因子 r_factor	—
R_work r_work	0.1890
R_free r_free	0.2280

fit	/app/data/saxs_computation/ie/1ieq/1ieq.fit
pddf	/app/data/pr_computation/ie/1ieq/1ieq.pr.out
profile	/app/data/saxs_computation/ie/1ieq/1ieq.dat

CRYSTAL STRUCTURE OF BARLEY BETA-D-GLUCAN GLUCOHYDROLASE ISOENZYME EXO1

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

1. 结构基本信息 1. Structure Basics

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

4. 晶体学与实验 4. Crystallography & Experiment

晶胞参数 Unit Cell

对称性 Symmetry

精修参数 Refinement

衍射实验 Diffraction