SAXSdb — 1hl9

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1hl9
沉积日期 deposition_date	2003-03-14
结构标题 title	CRYSTAL STRUCTURE OF THERMOTOGA MARITIMA ALPHA-FUCOSIDASE IN COMPLEX WITH A MECHANISM BASED INHIBITOR
关键词 keywords	HYDROLASE, GLYCOSIDE HYDROLASE, ALPHA-L-FUCOSIDASE, GLYCOSYL-ENZYME INTERMEDIATE, THERMOSTABLE; 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	34.84 Å
回转半径 Rg (电子) rg_electron	34.15 Å
零角强度 I(0) i0	140697000.00
分子量 molecular_weight	99267.0 kDa
排除体积 excluded_volume	125590 Å³
包络体积 envelope_volume	163490 Å³
水化壳体积 shell_volume	39524 Å³
包络直径 envelope_diameter	108.0 Å
壳层 Rg shell_rg	41.68 Å
包络 Rg envelope_rg	32.95 Å
形状 Rg shape_rg	34.07 Å
总 Rg total_rg	34.98 Å
总原子数 total_atoms	7051
残基数 n_residues	846
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	101.6 Å
Rg (实空间) rg_real	34.71 Å
Rg 误差 (实空间) rg_real_error	0.58 Å
I(0) (实空间) i0_real	1.4070e+08
I(0) 误差 (实空间) i0_real_error	2.0310e+06
Rg (倒空间) rg_reciprocal	34.80 Å
I(0) (倒空间) i0_reciprocal	140700000.0000
解质量估计 total_estimate	0.8869
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	54.2 Å
偏度 Skewness skewness	0.037
峰度 Kurtosis kurtosis	-0.831
角度范围 angular_range	— – 0.2250 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	28820000.0000
实空间数据点数 n_real_points	46
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.979; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.597

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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 (3)

Entity 1 polymer

描述 description	PUTATIVE ALPHA-L-FUCOSIDASE
分子量 formula_weight	52315.1 kDa
EC 编号 ec_number	3.2.1.51
来源方法 src_method	man
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	7280

MISMKPRYKPDWESLREHTVPKWFDKAKFGIFIHWGIYSVPGWATPTGELGKVPMDAWFFQNPYAEWYENSLRIKESPTWEYHVKTYGENFEYEKFADLFTAEKWDPQEWADLFKKAGAKYVIPTTKHHDGFCLWGTKYTDFNSVKRGPKRDLVGDLAKAVREAGLRFGVYYSGGLDWRFTTEPIRYPEDLSYIRPNTYEYADYAYKQVMELVDLYLPDVLWNDMGWPEKGKEDLKYLFAYYYNKHPEGSVNDRWGVPHWDFKTAEYHVNYPGDLPGYKWEFTRGIGLSFGYNRNEGPEHMLSVEQLVYTLVDVVSKGGNLLLNVGPKGDGTIPDLQKERLLGLGEWLRKYGDAIYGTSVWERCCAKTEDGTEIRFTRKCNRIFVIFLGIPTGEKIVIEDLNLSAGTVRHFLTGERLSFKNVGKNLEITVPKKLLETDSITLVLEAVEE

来源 Source

来源生物 organism	THERMOTOGA MARITIMA
NCBI 分类编号 ncbi_taxonomy_id	243274
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 non-polymer

描述 description	2-deoxy-2-fluoro-beta-L-fucopyranose
分子量 formula_weight	166.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 3 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	209

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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	d1hl9a1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.71 — Glycosyl hydrolase domain
超家族 Superfamily superfamily	b.71.1 — Glycosyl hydrolase domain
家族 Family family	b.71.1.3 — Putative alpha-L-fucosidase C-terminal domain

结构域编号 domain_id	d1hl9a2
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.1.8.11 — Putative alpha-L-fucosidase, catalytic domain

结构域编号 domain_id	d1hl9b1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.71 — Glycosyl hydrolase domain
超家族 Superfamily superfamily	b.71.1 — Glycosyl hydrolase domain
家族 Family family	b.71.1.3 — Putative alpha-L-fucosidase C-terminal domain

结构域编号 domain_id	d1hl9b2
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.1.8.11 — Putative alpha-L-fucosidase, catalytic domain

CATH v4.4 (4 domains)

结构域编号 domain_id	1hl9A01
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	80 — Glycosidases

结构域编号 domain_id	1hl9A02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	1180 — Golgi alpha-mannosidase II

结构域编号 domain_id	1hl9B01
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	80 — Glycosidases

结构域编号 domain_id	1hl9B02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	1180 — Golgi alpha-mannosidase II

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7. 引用文献 (1)

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晶胞边长 a length_a	172.157 Å
晶胞边长 b length_b	172.157 Å
晶胞边长 c length_c	167.331 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	120.00 °
晶胞分子数 Z z_pdb	36

空间群 space_group	H 3 2
空间群编号 int_tables_number	155
晶系 crystal_system	—

分辨率 resolution	2.250 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.1840
R_work r_work	0.1810
R_free r_free	0.2290

fit	/app/data/saxs_computation/hl/1hl9/1hl9.fit
pddf	/app/data/pr_computation/hl/1hl9/1hl9.pr.out
profile	/app/data/saxs_computation/hl/1hl9/1hl9.dat

CRYSTAL STRUCTURE OF THERMOTOGA MARITIMA ALPHA-FUCOSIDASE IN COMPLEX WITH A MECHANISM BASED INHIBITOR

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