1ju2

Crystal structure of the hydroxynitrile lyase from almond

Method: X-RAY DIFFRACTION D_max: 103.6 Å Quality: EXCELLENT

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	1ju2
沉积日期 deposition_date	2001-08-23
结构标题 title	Crystal structure of the hydroxynitrile lyase from almond
关键词 keywords	hydroxynitrile lyase, flavin, GMC oxidoreductase, almond, cyanogenesis, LYASE; LYASE
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	32.89 Å
回转半径 Rg (电子) rg_electron	32.06 Å
零角强度 I(0) i0	220792000.00
分子量 molecular_weight	119190.0 kDa
排除体积 excluded_volume	148820 Å³
包络体积 envelope_volume	177500 Å³
水化壳体积 shell_volume	44815 Å³
包络直径 envelope_diameter	103.6 Å
壳层 Rg shell_rg	40.22 Å
包络 Rg envelope_rg	31.74 Å
形状 Rg shape_rg	32.04 Å
总 Rg total_rg	32.74 Å
总原子数 total_atoms	8413
残基数 n_residues	1042
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	103.6 Å
Rg (实空间) rg_real	32.81 Å
Rg 误差 (实空间) rg_real_error	0.71 Å
I(0) (实空间) i0_real	2.2080e+08
I(0) 误差 (实空间) i0_real_error	3.5210e+06
Rg (倒空间) rg_reciprocal	32.85 Å
I(0) (倒空间) i0_reciprocal	220800000.0000
解质量估计 total_estimate	0.9053
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	34.5 Å
偏度 Skewness skewness	0.225
峰度 Kurtosis kurtosis	-0.650
角度范围 angular_range	— – 0.2400 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	133000000.0000
实空间数据点数 n_real_points	49
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.937; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.956

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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 (10)

Entity 1 polymer

描述 description	hydroxynitrile lyase
分子量 formula_weight	58090.7 kDa
EC 编号 ec_number	4.1.2.10
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	9995

LATTSDHDFSYLSFAYDATDLELEGSYDYVIVGGGTSGCPLAATLSEKYKVLVLERGSLPTAYPNVLTADGFVYNLQQEDDGKTPVERFVSEDGIDNVRGRVLGGTSIINAGVYARANTSIYSASGVDWDMDLVNQTYEWVEDTIVYKPNSQSWQSVTKTAFLEAGVHPNHGFSLDHEEGTRITGSTFDNKGTRHAADELLNKGNSNNLRVGVHASVEKIIFSNAPGLTATGVIYRDSNGTPHQAFVRSKGEVIVSAGTIGTPQLLLLSGVGPESYLSSLNIPVVLSHPYVGQFLHDNPRNFINILPPNPIEPTIVTVLGISNDFYQCSFSSLPFTTPPFGFFPSSSYPLPNSTFAHFASKVAGPLSYGSLTLKSSSNVRVSPNVKFNYYSNLTDLSHCVSGMKKIGELLSTDALKPYKVEDLPGVEGFNILGIPLPKDQTDDAAFETFCRESVASYWHYHGGCLVGKVLDGDFRVTGINALRVVDGSTFPYTPASHPQGFYLMLGRYVGIKILQERSASDLKILDSLKSAASLVL

Entity 2 branched

描述 description	2-acetamido-2-deoxy-alpha-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 3 branched

描述 description	;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	894.8 kDa
来源方法 src_method	man
拷贝数 entity_count	2

Entity 4 branched

描述 description	;beta-D-mannopyranose-(1-3)-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	894.8 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 5 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 6 branched

描述 description	;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	732.7 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 7 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	2

Entity 8 non-polymer

描述 description	FLAVIN-ADENINE DINUCLEOTIDE
分子量 formula_weight	785.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 9 non-polymer

描述 description	ISOPROPYL ALCOHOL
分子量 formula_weight	60.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 10 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	1516

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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	d1ju2a1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.3 — FAD/NAD(P)-binding domain
超家族 Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
家族 Family family	c.3.1.2 — FAD-linked reductases, N-terminal domain

结构域编号 domain_id	d1ju2a2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.16 — FAD-linked reductases, C-terminal domain
超家族 Superfamily superfamily	d.16.1 — FAD-linked reductases, C-terminal domain
家族 Family family	d.16.1.1 — GMC oxidoreductases

结构域编号 domain_id	d1ju2b1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.3 — FAD/NAD(P)-binding domain
超家族 Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
家族 Family family	c.3.1.2 — FAD-linked reductases, N-terminal domain

结构域编号 domain_id	d1ju2b2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.16 — FAD-linked reductases, C-terminal domain
超家族 Superfamily superfamily	d.16.1 — FAD-linked reductases, C-terminal domain
家族 Family family	d.16.1.1 — GMC oxidoreductases

CATH v4.4 (4 domains)

结构域编号 domain_id	1ju2A01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	50 — FAD/NAD(P)-binding domain
同源超家族 H-superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

结构域编号 domain_id	1ju2A02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	410 — Cholesterol Oxidase; domain 2
同源超家族 H-superfamily homologous superfamily	40 —

结构域编号 domain_id	1ju2B01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	50 — FAD/NAD(P)-binding domain
同源超家族 H-superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

结构域编号 domain_id	1ju2B02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	410 — Cholesterol Oxidase; domain 2
同源超家族 H-superfamily homologous superfamily	40 —

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7. 引用文献 (1)

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晶胞边长 a length_a	56.176 Å
晶胞边长 b length_b	67.494 Å
晶胞边长 c length_c	79.796 Å
晶胞夹角 α angle_alpha	79.57 °
晶胞夹角 β angle_beta	77.78 °
晶胞夹角 γ angle_gamma	67.19 °
晶胞分子数 Z z_pdb	2

空间群 space_group	P 1
空间群编号 int_tables_number	1
晶系 crystal_system	—

分辨率 resolution	1.470 Å
最低分辨率 resolution_low	23.230 Å
R 因子 r_factor	—
R_work r_work	0.1600
R_free r_free	0.1860

fit	/app/data/saxs_computation/ju/1ju2/1ju2.fit
pddf	/app/data/pr_computation/ju/1ju2/1ju2.pr.out
profile	/app/data/saxs_computation/ju/1ju2/1ju2.dat