1j8v

;Crystal structure of barley beta-D-glucan glucohydrolase isoenzyme Exo1 in complex with 4'-nitrophenyl 3I-thiolaminaritrioside ;

Method: X-RAY DIFFRACTION D_max: 90.6 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

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1j8v
沉积日期 deposition_date	2001-05-22
结构标题 title	;Crystal structure of barley beta-D-glucan glucohydrolase isoenzyme Exo1 in complex with 4'-nitrophenyl 3I-thiolaminaritrioside ;
关键词 keywords	2-domain fold, ligand-protein complex, HYDROLASE; HYDROLASE
实验方法 method	X-RAY DIFFRACTION

▼

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

回转半径 Rg (Guinier) rg_guinier	25.37 Å
回转半径 Rg (电子) rg_electron	24.76 Å
零角强度 I(0) i0	73585800.00
分子量 molecular_weight	67388.0 kDa
排除体积 excluded_volume	84380 Å³
包络体积 envelope_volume	95172 Å³
水化壳体积 shell_volume	31619 Å³
包络直径 envelope_diameter	92.8 Å
壳层 Rg shell_rg	32.64 Å
包络 Rg envelope_rg	25.20 Å
形状 Rg shape_rg	24.75 Å
总 Rg total_rg	25.58 Å
总原子数 total_atoms	4730
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

▼

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

最大尺寸 Dmax dmax	90.6 Å
Rg (实空间) rg_real	25.38 Å
Rg 误差 (实空间) rg_real_error	0.56 Å
I(0) (实空间) i0_real	7.3590e+07
I(0) 误差 (实空间) i0_real_error	1.0580e+06
Rg (倒空间) rg_reciprocal	25.38 Å
I(0) (倒空间) i0_reciprocal	73590000.0000
解质量估计 total_estimate	0.8379
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	28.8 Å
偏度 Skewness skewness	0.456
峰度 Kurtosis kurtosis	-0.073
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	22740000.0000
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: 0.654; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.928; Smooth: 0.999

▶

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

▶

5. 实体与聚合体信息 (6)

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	4999

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 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 non-polymer

描述 description	4'-NITROPHENYL-S-(BETA-D-GLUCOPYRANOSYL)-(1-3)-(3-THIO-BETA-D-GLUCOPYRANOSYL)-(1-3)-BETA-D-GLUCOPYRANOSIDE
分子量 formula_weight	641.6 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	269

▼

6. 折叠分类 (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d1j8va1
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	d1j8va2
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	1j8vA01
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	1j8vA02
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

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	100.533 Å
晶胞边长 b length_b	100.533 Å
晶胞边长 c length_c	181.959 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	2.400 Å
最低分辨率 resolution_low	10.000 Å
R 因子 r_factor	—
R_work r_work	0.2010
R_free r_free	0.2500

fit	/app/data/saxs_computation/j8/1j8v/1j8v.fit
pddf	/app/data/pr_computation/j8/1j8v/1j8v.pr.out
profile	/app/data/saxs_computation/j8/1j8v/1j8v.dat