SAXSdb — 2hor

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2hor
沉积日期 deposition_date	2006-07-16
结构标题 title	Crystal structure of alliinase from garlic- apo form
关键词 keywords	;alliinase; garlic; Allium sativum; glycosylation; plant enzyme; Pyridoxal-5'-phosphate; aminoacrylate; apo form;, 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	24.29 Å
回转半径 Rg (电子) rg_electron	23.11 Å
零角强度 I(0) i0	44410700.00
分子量 molecular_weight	50615.0 kDa
排除体积 excluded_volume	62847 Å³
包络体积 envelope_volume	77102 Å³
水化壳体积 shell_volume	27282 Å³
包络直径 envelope_diameter	85.6 Å
壳层 Rg shell_rg	30.77 Å
包络 Rg envelope_rg	23.59 Å
形状 Rg shape_rg	23.05 Å
总 Rg total_rg	24.18 Å
总原子数 total_atoms	3547
残基数 n_residues	425
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	77.3 Å
Rg (实空间) rg_real	24.18 Å
Rg 误差 (实空间) rg_real_error	0.58 Å
I(0) (实空间) i0_real	4.4410e+07
I(0) 误差 (实空间) i0_real_error	6.4770e+05
Rg (倒空间) rg_reciprocal	24.20 Å
I(0) (倒空间) i0_reciprocal	44410000.0000
解质量估计 total_estimate	0.8242
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	76.1 Å
偏度 Skewness skewness	0.212
峰度 Kurtosis kurtosis	-0.427
角度范围 angular_range	— – 0.3250 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	6916000.0000
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: 0.905; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

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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 (8)

Entity 1 polymer

描述 description	Alliin lyase 1
分子量 formula_weight	49056.6 kDa
EC 编号 ec_number	4.4.1.4
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	4122

KMTWTMKAAEEAEAVANINCSEHGRAFLDGIISEGSPKCECNTCYTGPDCSEKIQGCSADVASGDGLFLEEYWKQHKEASAVLVSPWHRMSYFFNPVSNFISFELEKTIKELHEVVGNAAAKDRYIVFGVGVTQLIHGLVISLSPNMTATPDAPESKVVAHAPFYPVFREQTKYFDKKGYVWAGNAANYVNVSNPEQYIEMVTSPNNPEGLLRHAVIKGCKSIYDMVYYWPHYTPIKYKADEDILLFTMSKFTGHSGSRFGWALIKDESVYNNLLNYMTKNTEGTPRETQLRSLKVLKEVVAMVKTQKGTMRDLNTFGFKKLRERWVNITALLDQSDRFSYQELPQSEYCNYFRRMRPPSPSYAWVKCEWEEDKDCYQTFQNGRINTQNGVGFEASSRYVRLSLIKTQDDFDQLMYYLKDMVKAKRK

Entity 2 branched

描述 description	;alpha-D-mannopyranose-(2-3)-[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	1057.0 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 3 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	1

Entity 4 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	5

Entity 5 non-polymer

描述 description	ACETATE ION
分子量 formula_weight	59.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 6 non-polymer

描述 description	CHLORIDE ION
分子量 formula_weight	35.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 7 non-polymer

描述 description	NITRATE ION
分子量 formula_weight	62.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 8 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	496

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6. 折叠分类 (SCOP + CATH) 4 domains

SCOP 2.08 (1 domains)

结构域编号 domain_id	d2hora_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.67 — PLP-dependent transferase-like
超家族 Superfamily superfamily	c.67.1 — PLP-dependent transferases
家族 Family family	c.67.1.1 — AAT-like

CATH v4.4 (3 domains)

结构域编号 domain_id	2horA01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	10 — Ribbon
拓扑 Topology topology	25 — Laminin
同源超家族 H-superfamily homologous superfamily	30 — EGF-like, alliinase

结构域编号 domain_id	2horA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	640 — Aspartate Aminotransferase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

结构域编号 domain_id	2horA03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1150 — Aspartate Aminotransferase, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aspartate Aminotransferase, domain 1

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7. 引用文献 (2)

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晶胞边长 a length_a	81.118 Å
晶胞边长 b length_b	81.118 Å
晶胞边长 c length_c	164.017 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 41 21 2
空间群编号 int_tables_number	92
晶系 crystal_system	—

分辨率 resolution	1.600 Å
最低分辨率 resolution_low	39.600 Å
R 因子 r_factor	0.1640
R_work r_work	0.1630
R_free r_free	0.1790

fit	/app/data/saxs_computation/ho/2hor/2hor.fit
pddf	/app/data/pr_computation/ho/2hor/2hor.pr.out
profile	/app/data/saxs_computation/ho/2hor/2hor.dat

Crystal structure of alliinase from garlic- apo form

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution