SAXSdb — 1tuy

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1tuy
沉积日期 deposition_date	2004-06-25
结构标题 title	Acetate Kinase complexed with ADP, AlF3 and acetate
关键词 keywords	alpha/beta, ASKHA (acetate and sugar kinases, hsc70, actin) superfamily, AlF3 and acetate, TRANSFERASE; TRANSFERASE
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	30.11 Å
回转半径 Rg (电子) rg_electron	29.79 Å
零角强度 I(0) i0	121689000.00
分子量 molecular_weight	87639.0 kDa
排除体积 excluded_volume	109730 Å³
包络体积 envelope_volume	132420 Å³
水化壳体积 shell_volume	38014 Å³
包络直径 envelope_diameter	116.7 Å
壳层 Rg shell_rg	36.00 Å
包络 Rg envelope_rg	30.17 Å
形状 Rg shape_rg	29.75 Å
总 Rg total_rg	30.42 Å
总原子数 total_atoms	6133
残基数 n_residues	797
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	108.4 Å
Rg (实空间) rg_real	30.28 Å
Rg 误差 (实空间) rg_real_error	0.88 Å
I(0) (实空间) i0_real	1.2170e+08
I(0) 误差 (实空间) i0_real_error	2.0050e+06
Rg (倒空间) rg_reciprocal	30.21 Å
I(0) (倒空间) i0_reciprocal	121700000.0000
解质量估计 total_estimate	0.8253
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	32.7 Å
偏度 Skewness skewness	0.614
峰度 Kurtosis kurtosis	0.162
角度范围 angular_range	— – 0.2650 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	31680000.0000
实空间数据点数 n_real_points	54
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.624; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.914; Smooth: 0.938

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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 (6)

Entity 1 polymer

描述 description	Acetate kinase
分子量 formula_weight	43411.8 kDa
EC 编号 ec_number	2.7.2.1
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	6182

MKVLVINAGSSSLKYQLIDMTNESALAVGLCERIGIDNSIITQKKFDGKKLEKLTDLPTHKDALEEVVKALTDDEFGVIKDMGEINAVGHRVVHGGEKFTTSALYDEGVEKAIKDCFELAPLHNPPNMMGISACAEIMPGTPMVIVFDTAFHQTMPPYAYMYALPYDLYEKHGVRKYGFHGTSHKYVAERAALMLGKPAEETKIITCHLGNGSSITAVEGGKSVETSMGFTPLEGLAMGTRCGSIDPAIVPFLMEKEGLTTREIDTLMNKKSGVLGVSGLSNDFRDLDEAASKGNRKAELALEIFAYKVKKFIGEYSAVLNGADAVVFTAGIGENSASIRKRILTGLDGIGIKIDDEKNKIRGQEIDISTPDAKVRVFVIPTNEELAIARETKEIVETE

来源 Source

来源生物 organism	Methanosarcina thermophila
NCBI 分类编号 ncbi_taxonomy_id	2210
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 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	1

Entity 3 non-polymer

描述 description	ADENOSINE-5'-DIPHOSPHATE
分子量 formula_weight	427.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 non-polymer

描述 description	ALUMINUM FLUORIDE
分子量 formula_weight	84.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 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	1

Entity 6 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	49

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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	d1tuya1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.55 — Ribonuclease H-like motif
超家族 Superfamily superfamily	c.55.1 — Actin-like ATPase domain
家族 Family family	c.55.1.2 — Acetokinase-like

结构域编号 domain_id	d1tuya2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.55 — Ribonuclease H-like motif
超家族 Superfamily superfamily	c.55.1 — Actin-like ATPase domain
家族 Family family	c.55.1.2 — Acetokinase-like

结构域编号 domain_id	d1tuyb1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.55 — Ribonuclease H-like motif
超家族 Superfamily superfamily	c.55.1 — Actin-like ATPase domain
家族 Family family	c.55.1.2 — Acetokinase-like

结构域编号 domain_id	d1tuyb2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.55 — Ribonuclease H-like motif
超家族 Superfamily superfamily	c.55.1 — Actin-like ATPase domain
家族 Family family	c.55.1.2 — Acetokinase-like

CATH v4.4 (4 domains)

结构域编号 domain_id	1tuyA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	420 — Nucleotidyltransferase; domain 5
同源超家族 H-superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

结构域编号 domain_id	1tuyA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	420 — Nucleotidyltransferase; domain 5
同源超家族 H-superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

结构域编号 domain_id	1tuyB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	420 — Nucleotidyltransferase; domain 5
同源超家族 H-superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

结构域编号 domain_id	1tuyB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	420 — Nucleotidyltransferase; domain 5
同源超家族 H-superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

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7. 引用文献 (1)

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晶胞边长 a length_a	180.043 Å
晶胞边长 b length_b	67.196 Å
晶胞边长 c length_c	82.142 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	103.13 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	—

分辨率 resolution	3.000 Å
最低分辨率 resolution_low	28.430 Å
R 因子 r_factor	0.2010
R_work r_work	0.2010
R_free r_free	0.2630

fit	/app/data/saxs_computation/tu/1tuy/1tuy.fit
pddf	/app/data/pr_computation/tu/1tuy/1tuy.pr.out
profile	/app/data/saxs_computation/tu/1tuy/1tuy.dat

Acetate Kinase complexed with ADP, AlF3 and acetate

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution