SAXSdb — 1q8f

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1q8f
沉积日期 deposition_date	2003-08-21
结构标题 title	Crystal Structure of the E.coli pyrimidine nucleoside hydrolase yeiK
关键词 keywords	open alpha-beta structure, NH-fold, HYDROLASE; 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	34.59 Å
回转半径 Rg (电子) rg_electron	33.96 Å
零角强度 I(0) i0	267999000.00
分子量 molecular_weight	133930.0 kDa
排除体积 excluded_volume	168230 Å³
包络体积 envelope_volume	196450 Å³
水化壳体积 shell_volume	46913 Å³
包络直径 envelope_diameter	110.8 Å
壳层 Rg shell_rg	41.74 Å
包络 Rg envelope_rg	33.96 Å
形状 Rg shape_rg	33.99 Å
总 Rg total_rg	34.39 Å
总原子数 total_atoms	9360
残基数 n_residues	1232
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	112.1 Å
Rg (实空间) rg_real	34.49 Å
Rg 误差 (实空间) rg_real_error	0.80 Å
I(0) (实空间) i0_real	2.6800e+08
I(0) 误差 (实空间) i0_real_error	4.0090e+06
Rg (倒空间) rg_reciprocal	34.55 Å
I(0) (倒空间) i0_reciprocal	268000000.0000
解质量估计 total_estimate	0.9010
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	46.3 Å
偏度 Skewness skewness	0.165
峰度 Kurtosis kurtosis	-0.622
角度范围 angular_range	— – 0.2300 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	213500000.0000
实空间数据点数 n_real_points	47
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.908; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.985

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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 (4)

Entity 1 polymer

描述 description	Pyrimidine nucleoside hydrolase
分子量 formula_weight	33761.9 kDa
EC 编号 ec_number	3.2.2.8
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	10415

MEKRKIILDCDPGHDDAIAIMMAAKHPAIDLLGITIVAGNQTLDKTLINGLNVCQKLEINVPVYAGMPQPIMRQQIVADNIHGDTGLDGPVFEPLTRQAESTHAVKYIIDTLMASDGDITLVPVGPLSNIAVAMRMQPAILPKIREIVLMGGAYGTGNFTPSAEFNIFADPEAARVVFTSGVPLVMMGLDLTNQTVCTPDVIARMERAGGPAGELFSDIMNFTLKTQFENYGLAGGPVHDATCIGYLINPDGIKTQEMYVEVDVNSGPCYGRTVCDELGVLGKPANTKVGITIDTDWFWGLVEECVRGYIKTH

来源 Source

来源生物 organism	Escherichia coli
NCBI 分类编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

描述 description	CALCIUM ION
分子量 formula_weight	40.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 3 non-polymer

描述 description	GLYCEROL
分子量 formula_weight	92.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	16

Entity 4 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	1055

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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	d1q8fa_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.70 — Nucleoside hydrolase
超家族 Superfamily superfamily	c.70.1 — Nucleoside hydrolase
家族 Family family	c.70.1.1 — Nucleoside hydrolase

结构域编号 domain_id	d1q8fb_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.70 — Nucleoside hydrolase
超家族 Superfamily superfamily	c.70.1 — Nucleoside hydrolase
家族 Family family	c.70.1.1 — Nucleoside hydrolase

结构域编号 domain_id	d1q8fc_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.70 — Nucleoside hydrolase
超家族 Superfamily superfamily	c.70.1 — Nucleoside hydrolase
家族 Family family	c.70.1.1 — Nucleoside hydrolase

结构域编号 domain_id	d1q8fd_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.70 — Nucleoside hydrolase
超家族 Superfamily superfamily	c.70.1 — Nucleoside hydrolase
家族 Family family	c.70.1.1 — Nucleoside hydrolase

CATH v4.4 (4 domains)

结构域编号 domain_id	1q8fA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	245 — Inosine-uridine Nucleoside N-ribohydrolase; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Ribonucleoside hydrolase-like

结构域编号 domain_id	1q8fB00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	245 — Inosine-uridine Nucleoside N-ribohydrolase; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Ribonucleoside hydrolase-like

结构域编号 domain_id	1q8fC00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	245 — Inosine-uridine Nucleoside N-ribohydrolase; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Ribonucleoside hydrolase-like

结构域编号 domain_id	1q8fD00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	245 — Inosine-uridine Nucleoside N-ribohydrolase; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Ribonucleoside hydrolase-like

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7. 引用文献 (4)

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晶胞边长 a length_a	44.808 Å
晶胞边长 b length_b	85.707 Å
晶胞边长 c length_c	90.678 Å
晶胞夹角 α angle_alpha	112.95 °
晶胞夹角 β angle_beta	101.95 °
晶胞夹角 γ angle_gamma	85.92 °
晶胞分子数 Z z_pdb	4

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

分辨率 resolution	1.700 Å
最低分辨率 resolution_low	43.830 Å
R 因子 r_factor	0.1535
R_work r_work	0.1533
R_free r_free	0.1699

fit	/app/data/saxs_computation/q8/1q8f/1q8f.fit
pddf	/app/data/pr_computation/q8/1q8f/1q8f.pr.out
profile	/app/data/saxs_computation/q8/1q8f/1q8f.dat

Crystal Structure of the E.coli pyrimidine nucleoside hydrolase yeiK

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