SAXSdb — 1nkq

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1nkq
沉积日期 deposition_date	2003-01-03
结构标题 title	Crystal structure of yeast ynq8, a fumarylacetoacetate hydrolase family protein
关键词 keywords	;dimer, PSI, Protein Structure Initiative, New York SGX Research Center for Structural Genomics, NYSGXRC, Structural Genomics, Unknown Function ;; Structural Genomics, Unknown Function
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	41.71 Å
回转半径 Rg (电子) rg_electron	41.75 Å
零角强度 I(0) i0	407983000.00
分子量 molecular_weight	164560.0 kDa
排除体积 excluded_volume	204980 Å³
包络体积 envelope_volume	258870 Å³
水化壳体积 shell_volume	53791 Å³
包络直径 envelope_diameter	144.3 Å
壳层 Rg shell_rg	44.84 Å
包络 Rg envelope_rg	41.49 Å
形状 Rg shape_rg	41.78 Å
总 Rg total_rg	41.82 Å
总原子数 total_atoms	11454
残基数 n_residues	1436
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	141.4 Å
Rg (实空间) rg_real	41.96 Å
Rg 误差 (实空间) rg_real_error	1.37 Å
I(0) (实空间) i0_real	4.0800e+08
I(0) 误差 (实空间) i0_real_error	7.8960e+06
Rg (倒空间) rg_reciprocal	41.71 Å
I(0) (倒空间) i0_reciprocal	407900000.0000
解质量估计 total_estimate	0.7792
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	37.2 Å
偏度 Skewness skewness	0.470
峰度 Kurtosis kurtosis	-0.546
角度范围 angular_range	— – 0.1900 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	129500000.0000
实空间数据点数 n_real_points	39
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.742; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.898; 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 (5)

Entity 1 polymer

描述 description	Hypothetical 28.8 kDa protein in PSD1-SKO1 intergenic region
分子量 formula_weight	29111.4 kDa
来源方法 src_method	man
拷贝数 entity_count	6

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F
原子数 atom_count	12088

MSYNYLKAARKIICIGRNYAAHIKELNNSTPKQPFFFLKPTSSIVTPLSSSLVKTTRPANSTFNGLNEDGTNPGPIFIPRGVKVHHEIELALIVSKHLSNVTKMKPEEVYDSISGVALALDLTARNVQDEAKKKGLPWTISKGFDTFMPISAIVSREKFSSYKSNLQDIFRVKCSVNGQLRQDGGTNLMLHPLHKILQHISTMISLEPGDIILTGTPAGVGELKPGDRVHCELLQNNDNIVDMNFECENRPGPYEFRET

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;baker's yeast ;
NCBI 分类编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli

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	6

Entity 3 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	7

Entity 4 non-polymer

描述 description	ACETIC ACID
分子量 formula_weight	60.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	12

Entity 5 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	634

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6. 折叠分类 (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

结构域编号 domain_id	d1nkqa_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.177 — FAH
超家族 Superfamily superfamily	d.177.1 — FAH
家族 Family family	d.177.1.1 — FAH

结构域编号 domain_id	d1nkqb_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.177 — FAH
超家族 Superfamily superfamily	d.177.1 — FAH
家族 Family family	d.177.1.1 — FAH

结构域编号 domain_id	d1nkqc_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.177 — FAH
超家族 Superfamily superfamily	d.177.1 — FAH
家族 Family family	d.177.1.1 — FAH

结构域编号 domain_id	d1nkqd_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.177 — FAH
超家族 Superfamily superfamily	d.177.1 — FAH
家族 Family family	d.177.1.1 — FAH

结构域编号 domain_id	d1nkqe_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.177 — FAH
超家族 Superfamily superfamily	d.177.1 — FAH
家族 Family family	d.177.1.1 — FAH

结构域编号 domain_id	d1nkqf_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.177 — FAH
超家族 Superfamily superfamily	d.177.1 — FAH
家族 Family family	d.177.1.1 — FAH

CATH v4.4 (6 domains)

结构域编号 domain_id	1nkqA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	850 — Fumarylacetoacetate hydrolase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Fumarylacetoacetase-like, C-terminal domain

结构域编号 domain_id	1nkqB00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	850 — Fumarylacetoacetate hydrolase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Fumarylacetoacetase-like, C-terminal domain

结构域编号 domain_id	1nkqC00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	850 — Fumarylacetoacetate hydrolase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Fumarylacetoacetase-like, C-terminal domain

结构域编号 domain_id	1nkqD00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	850 — Fumarylacetoacetate hydrolase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Fumarylacetoacetase-like, C-terminal domain

结构域编号 domain_id	1nkqE00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	850 — Fumarylacetoacetate hydrolase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Fumarylacetoacetase-like, C-terminal domain

结构域编号 domain_id	1nkqF00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	850 — Fumarylacetoacetate hydrolase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Fumarylacetoacetase-like, C-terminal domain

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7. 引用文献 (1)

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晶胞边长 a length_a	57.705 Å
晶胞边长 b length_b	85.990 Å
晶胞边长 c length_c	316.704 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	24

空间群 space_group	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	2.200 Å
最低分辨率 resolution_low	50.000 Å
R 因子 r_factor	—
R_work r_work	0.2160
R_free r_free	0.2620

fit	/app/data/saxs_computation/nk/1nkq/1nkq.fit
pddf	/app/data/pr_computation/nk/1nkq/1nkq.pr.out
profile	/app/data/saxs_computation/nk/1nkq/1nkq.dat

Crystal structure of yeast ynq8, a fumarylacetoacetate hydrolase family protein

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