SAXSdb — 1gai

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1gai
沉积日期 deposition_date	1996-03-06
结构标题 title	GLUCOAMYLASE-471 COMPLEXED WITH D-GLUCO-DIHYDROACARBOSE
关键词 keywords	HYDROLASE, GLYCOSIDASE, POLYSACCHARIDE DEGRADATION, GLYCOPROTEIN; 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	22.66 Å
回转半径 Rg (电子) rg_electron	21.44 Å
零角强度 I(0) i0	53209800.00
分子量 molecular_weight	55282.0 kDa
排除体积 excluded_volume	68271 Å³
包络体积 envelope_volume	76206 Å³
水化壳体积 shell_volume	28414 Å³
包络直径 envelope_diameter	71.9 Å
壳层 Rg shell_rg	29.57 Å
包络 Rg envelope_rg	21.67 Å
形状 Rg shape_rg	21.39 Å
总 Rg total_rg	22.44 Å
总原子数 total_atoms	4970
残基数 n_residues	472
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	69.2 Å
Rg (实空间) rg_real	22.50 Å
Rg 误差 (实空间) rg_real_error	0.30 Å
I(0) (实空间) i0_real	5.3210e+07
I(0) 误差 (实空间) i0_real_error	6.7300e+05
Rg (倒空间) rg_reciprocal	22.54 Å
I(0) (倒空间) i0_reciprocal	53210000.0000
解质量估计 total_estimate	0.9005
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	29.4 Å
偏度 Skewness skewness	0.108
峰度 Kurtosis kurtosis	-0.468
角度范围 angular_range	— – 0.3500 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	18520000.0000
实空间数据点数 n_real_points	67
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.913; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.976; Smooth: 0.988

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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	GLUCOAMYLASE-471
分子量 formula_weight	50608.9 kDa
EC 编号 ec_number	3.2.1.3
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	6927

ATLDSWLSNEATVARTAILNNIGADGAWVSGADSGIVVASPSTDNPDYFYTWTRDSGLVIKTLVDLFRNGDTDLLSTIEHYISSQAIIQGVSNPSGDLSSGGLGEPKFNVDETAYTGSWGRPQRDGPALRATAMIGFGQWLLDNGYTSAATEIVWPLVRNDLSYVAQYWNQTGYDLWEEVNGSSFFTIAVQHRALVEGSAFATAVGSSCSWCDSQAPQILCYLQSFWTGSYILANFDSSRSGKDTNTLLGSIHTFDPEAGCDDSTFQPCSPRALANHKEVVDSFRSIYTLNDGLSDSEAVAVGRYPEDSYYNGNPWFLCTLAAAEQLYDALYQWDKQGSLEITDVSLDFFKALYSGAATGTYSSSSSTYSSIVSAVKTFADGFVSIVETHAASNGSLSEQFDKSDGDELSARDLTWSYAALLTANNRRNSVVPPSWGETSASSVPGTCAATSASGTYSSVTVTSWPSIVATG

Entity 2 branched

描述 description	;alpha-D-mannopyranose-(1-2)-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	910.8 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-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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	1559.4 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 4 branched

描述 description	;4,6-dideoxy-4-{[(1S,2S,3S,4R,5R)-2,3,4-trihydroxy-5-(hydroxymethyl)cyclohexyl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose ;
分子量 formula_weight	647.6 kDa
来源方法 src_method	man
拷贝数 entity_count	1

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	10

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	551

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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	d1gaia_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.102 — alpha/alpha toroid
超家族 Superfamily superfamily	a.102.1 — Six-hairpin glycosidases
家族 Family family	a.102.1.1 — Glucoamylase

CATH v4.4 (1 domains)

结构域编号 domain_id	1gaiA00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	50 — Alpha/alpha barrel
拓扑 Topology topology	10 — Glycosyltransferase
同源超家族 H-superfamily homologous superfamily	10 —

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7. 引用文献 (6)

;Crystallographic complexes of glucoamylase with maltooligosaccharide analogs: relationship of stereochemical distortions at the nonreducing end to the catalytic mechanism. ;

Biochemistry (1996)

PMID: 8679589 · DOI: 10.1021/bi960321g PRIMARY

;Refined Structure for the Complex of D-Gluco-Dihydroacarbose with Glucoamylase from Aspergillus Awamori Var. X100 to 2.2 A Resolution: Dual Conformations for Extended Inhibitors Bound to the Active Site of Glucoamylase ;

FEBS Lett. (1995)

Refined Crystal Structures of Glucoamylase from Aspergillus Awamori Var. X100

J.Mol.Biol. (1994)

Refined Structure for the Complex of Acarbose with Glucoamylase from Aspergillus Awamori Var. X100 to 2.4-A Resolution

J.Biol.Chem. (1994)

Refined Structure for the Complex of 1-Deoxynojirimycin with Glucoamylase from Aspergillus Awamori Var. X100 to 2.4-A Resolution

Biochemistry (1993)

Crystal Structure of Glucoamylase from Aspergillus Awamori Var. X100 to 2.2-A Resolution

J.Biol.Chem. (1992)

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晶胞边长 a length_a	116.900 Å
晶胞边长 b length_b	104.400 Å
晶胞边长 c length_c	48.400 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 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	1.700 Å
最低分辨率 resolution_low	10.000 Å
R 因子 r_factor	0.1470
R_work r_work	0.1470
R_free r_free	0.1670

fit	/app/data/saxs_computation/ga/1gai/1gai.fit
pddf	/app/data/pr_computation/ga/1gai/1gai.pr.out
profile	/app/data/saxs_computation/ga/1gai/1gai.dat

GLUCOAMYLASE-471 COMPLEXED WITH D-GLUCO-DIHYDROACARBOSE

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