2ahu

Crystal structure of Acyl-CoA transferase (YdiF) apoenzyme from Escherichia coli O157:H7.

Method: X-RAY DIFFRACTION D_max: 127.5 Å Quality: EXCELLENT

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

下载 Download SAXS (.dat) P(r) (.pr.out) CIF

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2ahu
沉积日期 deposition_date	2005-07-28
结构标题 title	Crystal structure of Acyl-CoA transferase (YdiF) apoenzyme from Escherichia coli O157:H7.
关键词 keywords	;YdiF, CoA transferase, Glutamyl thioester, Structural Genomics, Montreal-Kingston Bacterial Structural Genomics Initiative, BSGI, 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	40.81 Å
回转半径 Rg (电子) rg_electron	40.47 Å
零角强度 I(0) i0	732523000.00
分子量 molecular_weight	224970.0 kDa
排除体积 excluded_volume	282130 Å³
包络体积 envelope_volume	358660 Å³
水化壳体积 shell_volume	71573 Å³
包络直径 envelope_diameter	125.3 Å
壳层 Rg shell_rg	47.76 Å
包络 Rg envelope_rg	40.22 Å
形状 Rg shape_rg	40.50 Å
总 Rg total_rg	40.72 Å
总原子数 total_atoms	15696
残基数 n_residues	2020
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	127.5 Å
Rg (实空间) rg_real	40.66 Å
Rg 误差 (实空间) rg_real_error	1.04 Å
I(0) (实空间) i0_real	7.3250e+08
I(0) 误差 (实空间) i0_real_error	1.2300e+07
Rg (倒空间) rg_reciprocal	40.81 Å
I(0) (倒空间) i0_reciprocal	732600000.0000
解质量估计 total_estimate	0.9090
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	49.0 Å
偏度 Skewness skewness	0.142
峰度 Kurtosis kurtosis	-0.662
角度范围 angular_range	— – 0.1950 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	146600000.0000
实空间数据点数 n_real_points	40
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.949; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.967

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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 (2)

Entity 1 polymer

描述 description	putative enzyme ydiF
分子量 formula_weight	58082.8 kDa
EC 编号 ec_number	2.8.3.-
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	16967

MKPVKPPRINGRVPVLSAQEAVNYIPDEATLCVLGAGGGILEATTLITALADKYKQTQTPRNLSIISPTGLGDRADRGISPLAQEGLVKWALCGHWGQSPRISDLAEQNKIIAYNYPQGVLTQTLRAAAAHQPGIISDIGIGTFVDPRQQGGKLNEVTKEDLIKLVEFDNKEYLYYKAIAPDIAFIRATTCDSEGYATFEDEVMYLDALVIAQAVHNNGGIVMMQVQKMVKKATLHPKSVRIPGYLVDIVVVDPDQSQLYGGAPVNRFISGDFTLDDSTKLSLPLNQRKLVARRALFEMRKGAVGNVGVGIADGIGLVAREEGCADDFILTVETGPIGGITSQGIAFGANVNTRAILDMTSQFDFYHGGGLDVCYLSFAEVDQHGNVGVHKFNGKIMGTGGFIDISATSKKIIFCGTLTAGSLKTEIADGKLNIVQEGRVKKFIRELPEITFSGKIALERGLDVRYITERAVFTLKEDGLHLIEIAPGVDLQKDILDKMDFTPVISPELKLMDERLFIDAAMGFVLPEAAH

来源 Source

来源生物 organism	Escherichia coli
NCBI 分类编号 ncbi_taxonomy_id	83334
宿主生物 host_organism	Escherichia coli

Entity 2 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	1271

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6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d2ahua1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.124 — NagB/RpiA/CoA transferase-like
超家族 Superfamily superfamily	c.124.1 — NagB/RpiA/CoA transferase-like
家族 Family family	c.124.1.3 — CoA transferase beta subunit-like

结构域编号 domain_id	d2ahua2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.124 — NagB/RpiA/CoA transferase-like
超家族 Superfamily superfamily	c.124.1 — NagB/RpiA/CoA transferase-like
家族 Family family	c.124.1.2 — CoA transferase alpha subunit-like

结构域编号 domain_id	d2ahub1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.124 — NagB/RpiA/CoA transferase-like
超家族 Superfamily superfamily	c.124.1 — NagB/RpiA/CoA transferase-like
家族 Family family	c.124.1.3 — CoA transferase beta subunit-like

结构域编号 domain_id	d2ahub2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.124 — NagB/RpiA/CoA transferase-like
超家族 Superfamily superfamily	c.124.1 — NagB/RpiA/CoA transferase-like
家族 Family family	c.124.1.2 — CoA transferase alpha subunit-like

结构域编号 domain_id	d2ahuc1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.124 — NagB/RpiA/CoA transferase-like
超家族 Superfamily superfamily	c.124.1 — NagB/RpiA/CoA transferase-like
家族 Family family	c.124.1.3 — CoA transferase beta subunit-like

结构域编号 domain_id	d2ahuc2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.124 — NagB/RpiA/CoA transferase-like
超家族 Superfamily superfamily	c.124.1 — NagB/RpiA/CoA transferase-like
家族 Family family	c.124.1.2 — CoA transferase alpha subunit-like

结构域编号 domain_id	d2ahud1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.124 — NagB/RpiA/CoA transferase-like
超家族 Superfamily superfamily	c.124.1 — NagB/RpiA/CoA transferase-like
家族 Family family	c.124.1.3 — CoA transferase beta subunit-like

结构域编号 domain_id	d2ahud2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.124 — NagB/RpiA/CoA transferase-like
超家族 Superfamily superfamily	c.124.1 — NagB/RpiA/CoA transferase-like
家族 Family family	c.124.1.2 — CoA transferase alpha subunit-like

CATH v4.4 (8 domains)

结构域编号 domain_id	2ahuA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1080 — Glutaconate Coenzyme A-transferase
同源超家族 H-superfamily homologous superfamily	10 — Glutaconate Coenzyme A-transferase

结构域编号 domain_id	2ahuA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1080 — Glutaconate Coenzyme A-transferase
同源超家族 H-superfamily homologous superfamily	10 — Glutaconate Coenzyme A-transferase

结构域编号 domain_id	2ahuB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1080 — Glutaconate Coenzyme A-transferase
同源超家族 H-superfamily homologous superfamily	10 — Glutaconate Coenzyme A-transferase

结构域编号 domain_id	2ahuB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1080 — Glutaconate Coenzyme A-transferase
同源超家族 H-superfamily homologous superfamily	10 — Glutaconate Coenzyme A-transferase

结构域编号 domain_id	2ahuC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1080 — Glutaconate Coenzyme A-transferase
同源超家族 H-superfamily homologous superfamily	10 — Glutaconate Coenzyme A-transferase

结构域编号 domain_id	2ahuC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1080 — Glutaconate Coenzyme A-transferase
同源超家族 H-superfamily homologous superfamily	10 — Glutaconate Coenzyme A-transferase

结构域编号 domain_id	2ahuD01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1080 — Glutaconate Coenzyme A-transferase
同源超家族 H-superfamily homologous superfamily	10 — Glutaconate Coenzyme A-transferase

结构域编号 domain_id	2ahuD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1080 — Glutaconate Coenzyme A-transferase
同源超家族 H-superfamily homologous superfamily	10 — Glutaconate Coenzyme A-transferase

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7. 引用文献 (1)

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晶胞边长 a length_a	81.129 Å
晶胞边长 b length_b	133.308 Å
晶胞边长 c length_c	105.838 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	100.57 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	—

分辨率 resolution	1.900 Å
最低分辨率 resolution_low	50.000 Å
R 因子 r_factor	0.1903
R_work r_work	0.1871
R_free r_free	0.2204

fit	/app/data/saxs_computation/ah/2ahu/2ahu.fit
pddf	/app/data/pr_computation/ah/2ahu/2ahu.pr.out
profile	/app/data/saxs_computation/ah/2ahu/2ahu.dat