1p4a

Crystal Structure of the PurR complexed with cPRPP

Method: X-RAY DIFFRACTION D_max: 123.2 Å Quality: GOOD

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	1p4a
沉积日期 deposition_date	2003-04-22
结构标题 title	Crystal Structure of the PurR complexed with cPRPP
关键词 keywords	TRANSCRIPTION; TRANSCRIPTION
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	36.35 Å
回转半径 Rg (电子) rg_electron	35.98 Å
零角强度 I(0) i0	208664000.00
分子量 molecular_weight	119070.0 kDa
排除体积 excluded_volume	150320 Å³
包络体积 envelope_volume	196290 Å³
水化壳体积 shell_volume	46328 Å³
包络直径 envelope_diameter	122.8 Å
壳层 Rg shell_rg	41.59 Å
包络 Rg envelope_rg	35.50 Å
形状 Rg shape_rg	35.99 Å
总 Rg total_rg	36.31 Å
总原子数 total_atoms	8352
残基数 n_residues	1074
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	123.2 Å
Rg (实空间) rg_real	36.47 Å
Rg 误差 (实空间) rg_real_error	1.05 Å
I(0) (实空间) i0_real	2.0870e+08
I(0) 误差 (实空间) i0_real_error	3.5820e+06
Rg (倒空间) rg_reciprocal	36.40 Å
I(0) (倒空间) i0_reciprocal	208600000.0000
解质量估计 total_estimate	0.8693
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	39.2 Å
偏度 Skewness skewness	0.429
峰度 Kurtosis kurtosis	-0.401
角度范围 angular_range	— – 0.2200 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	40210000.0000
实空间数据点数 n_real_points	45
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.812; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.947; Smooth: 0.913

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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	Pur operon repressor
分子量 formula_weight	31260.9 kDa
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	8926

MKFRRSGRLVDLTNYLLTHPHELIPLTFFSERYESAKSSISEDLTIIKQTFEQQGIGTLLTVPGAAGGVKYIPKMKQAEAEEFVQTLGQSLANPERILPGGYVYLTDILGKPSVLSKVGKLFASVFAEREIDVVMTVATKGIPLAYAAASYLNVPVVIVRKDNKVTEGSTVSINYVSGSSNRIQTMSLAKRSMKTGSNVLIIDDFMKAGGTINGMINLLDEFNANVAGIGVLVEAEGVDERLVDEYMSLLTLSTINMKEKSIEIQNGNFLRFFKDNLLKNGETES

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	1-ALPHA-PYROPHOSPHORYL-2-ALPHA,3-ALPHA-DIHYDROXY-4-BETA-CYCLOPENTANE-METHANOL-5-PHOSPHATE
分子量 formula_weight	388.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

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	574

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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	d1p4aa1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
超家族 Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
家族 Family family	a.4.5.40 — N-terminal domain of Bacillus PurR

结构域编号 domain_id	d1p4aa2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.61 — PRTase-like
超家族 Superfamily superfamily	c.61.1 — PRTase-like
家族 Family family	c.61.1.1 — Phosphoribosyltransferases (PRTases)

结构域编号 domain_id	d1p4ab1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
超家族 Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
家族 Family family	a.4.5.40 — N-terminal domain of Bacillus PurR

结构域编号 domain_id	d1p4ab2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.61 — PRTase-like
超家族 Superfamily superfamily	c.61.1 — PRTase-like
家族 Family family	c.61.1.1 — Phosphoribosyltransferases (PRTases)

结构域编号 domain_id	d1p4ac1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
超家族 Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
家族 Family family	a.4.5.40 — N-terminal domain of Bacillus PurR

结构域编号 domain_id	d1p4ac2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.61 — PRTase-like
超家族 Superfamily superfamily	c.61.1 — PRTase-like
家族 Family family	c.61.1.1 — Phosphoribosyltransferases (PRTases)

结构域编号 domain_id	d1p4ad1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
超家族 Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
家族 Family family	a.4.5.40 — N-terminal domain of Bacillus PurR

结构域编号 domain_id	d1p4ad2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.61 — PRTase-like
超家族 Superfamily superfamily	c.61.1 — PRTase-like
家族 Family family	c.61.1.1 — Phosphoribosyltransferases (PRTases)

CATH v4.4 (8 domains)

结构域编号 domain_id	1p4aA01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	10 — Arc Repressor Mutant, subunit A
同源超家族 H-superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

结构域编号 domain_id	1p4aA02
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	2020 —

结构域编号 domain_id	1p4aB01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	10 — Arc Repressor Mutant, subunit A
同源超家族 H-superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

结构域编号 domain_id	1p4aB02
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	2020 —

结构域编号 domain_id	1p4aC01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	10 — Arc Repressor Mutant, subunit A
同源超家族 H-superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

结构域编号 domain_id	1p4aC02
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	2020 —

结构域编号 domain_id	1p4aD01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	10 — Arc Repressor Mutant, subunit A
同源超家族 H-superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

结构域编号 domain_id	1p4aD02
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	2020 —

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7. 引用文献 (1)

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晶胞边长 a length_a	58.371 Å
晶胞边长 b length_b	135.718 Å
晶胞边长 c length_c	82.071 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	95.10 °
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	2.220 Å
最低分辨率 resolution_low	37.800 Å
R 因子 r_factor	0.1803
R_work r_work	0.1773
R_free r_free	0.2337

fit	/app/data/saxs_computation/p4/1p4a/1p4a.fit
pddf	/app/data/pr_computation/p4/1p4a/1p4a.pr.out
profile	/app/data/saxs_computation/p4/1p4a/1p4a.dat