1td9

Crystal Structure of a Phosphotransacetylase from Bacillus subtilis

Method: X-RAY DIFFRACTION D_max: 156.9 Å Quality: REASONABLE

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	1td9
沉积日期 deposition_date	2004-05-21
结构标题 title	Crystal Structure of a Phosphotransacetylase from Bacillus subtilis
关键词 keywords	;structural genomics, BSGC structure funded by NIH, Protein Structure Initiative, PSI, Berkeley Structural Genomics Center, 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	45.22 Å
回转半径 Rg (电子) rg_electron	44.87 Å
零角强度 I(0) i0	663543000.00
分子量 molecular_weight	211140.0 kDa
排除体积 excluded_volume	264070 Å³
包络体积 envelope_volume	371910 Å³
水化壳体积 shell_volume	70041 Å³
包络直径 envelope_diameter	159.9 Å
壳层 Rg shell_rg	48.87 Å
包络 Rg envelope_rg	43.79 Å
形状 Rg shape_rg	44.85 Å
总 Rg total_rg	45.13 Å
总原子数 total_atoms	14802
残基数 n_residues	1941
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	156.9 Å
Rg (实空间) rg_real	45.22 Å
Rg 误差 (实空间) rg_real_error	1.96 Å
I(0) (实空间) i0_real	6.6350e+08
I(0) 误差 (实空间) i0_real_error	1.4080e+07
Rg (倒空间) rg_reciprocal	45.22 Å
I(0) (倒空间) i0_reciprocal	663500000.0000
解质量估计 total_estimate	0.6539
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	53.8 Å
偏度 Skewness skewness	0.299
峰度 Kurtosis kurtosis	-0.447
角度范围 angular_range	— – 0.1750 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	54370000.0000
实空间数据点数 n_real_points	36
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.847; Stabil: 1.000; Sysdev: 0.010; Positv: 1.000; Valcen: 0.968; Smooth: 0.956

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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	Phosphate acetyltransferase
分子量 formula_weight	35170.9 kDa
EC 编号 ec_number	2.3.1.8
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	14916

GGGGGGMADLFSTVQEKVAGKDVKIVFPEGLDERILEAVSKLAGNKVLNPIVIGNENEIQAKAKELNLTLGGVKIYDPHTYEGMEDLVQAFVERRKGKATEEQARKALLDENYFGTMLVYKGLADGLVSGAAHSTADTVRPALQIIKTKEGVKKTSGVFIMARGEEQYVFADCAINIAPDSQDLAEIAIESANTAKMFDIEPRVAMLSFSTKGSAKSDETEKVADAVKIAKEKAPELTLDGEFQFDAAFVPSVAEKKAPDSEIKGDANVFVFPSLEAGNIGYKIAQRLGNFEAVGPILQGLNMPVNDLSRGCNAEDVYNLALITAAQAL

来源 Source

来源生物 organism	Bacillus subtilis
NCBI 分类编号 ncbi_taxonomy_id	1423
宿主生物 host_organism	Escherichia coli

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	24

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	114

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6. 折叠分类 (SCOP + CATH) 20 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d1td9a_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.77 — Isocitrate/Isopropylmalate dehydrogenase-like
超家族 Superfamily superfamily	c.77.1 — Isocitrate/Isopropylmalate dehydrogenase-like
家族 Family family	c.77.1.5 — Phosphotransacetylase

结构域编号 domain_id	d1td9b1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.77 — Isocitrate/Isopropylmalate dehydrogenase-like
超家族 Superfamily superfamily	c.77.1 — Isocitrate/Isopropylmalate dehydrogenase-like
家族 Family family	c.77.1.5 — Phosphotransacetylase

结构域编号 domain_id	d1td9b2
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d1td9c_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.77 — Isocitrate/Isopropylmalate dehydrogenase-like
超家族 Superfamily superfamily	c.77.1 — Isocitrate/Isopropylmalate dehydrogenase-like
家族 Family family	c.77.1.5 — Phosphotransacetylase

结构域编号 domain_id	d1td9d1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.77 — Isocitrate/Isopropylmalate dehydrogenase-like
超家族 Superfamily superfamily	c.77.1 — Isocitrate/Isopropylmalate dehydrogenase-like
家族 Family family	c.77.1.5 — Phosphotransacetylase

结构域编号 domain_id	d1td9d2
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d1td9e_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.77 — Isocitrate/Isopropylmalate dehydrogenase-like
超家族 Superfamily superfamily	c.77.1 — Isocitrate/Isopropylmalate dehydrogenase-like
家族 Family family	c.77.1.5 — Phosphotransacetylase

结构域编号 domain_id	d1td9f_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.77 — Isocitrate/Isopropylmalate dehydrogenase-like
超家族 Superfamily superfamily	c.77.1 — Isocitrate/Isopropylmalate dehydrogenase-like
家族 Family family	c.77.1.5 — Phosphotransacetylase

CATH v4.4 (12 domains)

结构域编号 domain_id	1td9A01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	10950 —

结构域编号 domain_id	1td9A02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	10750 — Isocitrate/Isopropylmalate dehydrogenase-like

结构域编号 domain_id	1td9B01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	10950 —

结构域编号 domain_id	1td9B02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	10750 — Isocitrate/Isopropylmalate dehydrogenase-like

结构域编号 domain_id	1td9C01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	10950 —

结构域编号 domain_id	1td9C02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	10750 — Isocitrate/Isopropylmalate dehydrogenase-like

结构域编号 domain_id	1td9D01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	10950 —

结构域编号 domain_id	1td9D02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	10750 — Isocitrate/Isopropylmalate dehydrogenase-like

结构域编号 domain_id	1td9E01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	10950 —

结构域编号 domain_id	1td9E02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	10750 — Isocitrate/Isopropylmalate dehydrogenase-like

结构域编号 domain_id	1td9F01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	10950 —

结构域编号 domain_id	1td9F02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	10750 — Isocitrate/Isopropylmalate dehydrogenase-like

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7. 引用文献 (1)

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晶胞边长 a length_a	185.207 Å
晶胞边长 b length_b	185.207 Å
晶胞边长 c length_c	259.414 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	72

空间群 space_group	P 64 2 2
空间群编号 int_tables_number	181
晶系 crystal_system	—

分辨率 resolution	2.750 Å
最低分辨率 resolution_low	19.990 Å
R 因子 r_factor	0.2680
R_work r_work	0.2680
R_free r_free	0.2970

fit	/app/data/saxs_computation/td/1td9/1td9.fit
pddf	/app/data/pr_computation/td/1td9/1td9.pr.out
profile	/app/data/saxs_computation/td/1td9/1td9.dat