1gph

STRUCTURE OF THE ALLOSTERIC REGULATORY ENZYME OF PURINE BIOSYNTHESIS

Method: X-RAY DIFFRACTION D_max: 116.6 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	1gph
沉积日期 deposition_date	1994-04-20
结构标题 title	STRUCTURE OF THE ALLOSTERIC REGULATORY ENZYME OF PURINE BIOSYNTHESIS
关键词 keywords	TRANSFERASE, GLUTAMINE AMIDOTRANSFERASE; 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	38.75 Å
回转半径 Rg (电子) rg_electron	37.98 Å
零角强度 I(0) i0	678813000.00
分子量 molecular_weight	205950.0 kDa
排除体积 excluded_volume	254620 Å³
包络体积 envelope_volume	317950 Å³
水化壳体积 shell_volume	66579 Å³
包络直径 envelope_diameter	117.9 Å
壳层 Rg shell_rg	46.99 Å
包络 Rg envelope_rg	37.06 Å
形状 Rg shape_rg	37.96 Å
总 Rg total_rg	38.50 Å
总原子数 total_atoms	14676
残基数 n_residues	1860
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	116.6 Å
Rg (实空间) rg_real	38.51 Å
Rg 误差 (实空间) rg_real_error	0.55 Å
I(0) (实空间) i0_real	6.7880e+08
I(0) 误差 (实空间) i0_real_error	9.7380e+06
Rg (倒空间) rg_reciprocal	38.66 Å
I(0) (倒空间) i0_reciprocal	678900000.0000
解质量估计 total_estimate	0.9070
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	48.4 Å
偏度 Skewness skewness	0.082
峰度 Kurtosis kurtosis	-0.699
角度范围 angular_range	— – 0.2050 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	262700000.0000
实空间数据点数 n_real_points	42
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.971; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.885

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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	GLUTAMINE PHOSPHORIBOSYL-PYROPHOSPHATE AMIDOTRANSFERASE
分子量 formula_weight	50507.2 kDa
EC 编号 ec_number	2.4.2.14
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	1,2,3,4
原子数 atom_count	14676

CGVFGIWGHEEAPQITYYGLHSLQHRGQEGAGIVATDGEKLTAHKGQGLITEVFQNGELSKVKGKGAIGHVRYATAGGGGYENVQPLLFRSQNNGSLALAHNGNLVNATQLKQQLENQGSIFQTSSDTEVLAHLIKRSGHFTLKDQIKNSLSMLKGAYAFLIMTETEMIVALDPNGLRPLSIGMMGDAYVVASETCAFDVVGATYLREVEPGEMLIINDEGMKSERFSMNINRSICSMEYIYFSRPDSNIDGINVHSARKNLGKMLAQESAVEADVVTGVPDSSISAAIGYAEATGIPYELGLIKNRYVGRTFIQPSQALREQGVRMKLSAVRGVVEGKRVVMVDDSIVRGTTSRRIVTMLREAGATEVHVKISSPPIAHPCFYGIDTSTHEELIASSHSVDEIRQEIGADTLSFLSVEGLLKGIGRKYDDSNCGQCLACFTGKYPTEIYQDTVLPHVKEAVLTK

来源 Source

来源生物 organism	Bacillus subtilis
NCBI 分类编号 ncbi_taxonomy_id	1423

Entity 2 non-polymer

描述 description	IRON/SULFUR CLUSTER
分子量 formula_weight	351.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 3 non-polymer

描述 description	ADENOSINE MONOPHOSPHATE
分子量 formula_weight	347.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	8

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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	d1gph11
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	d1gph12
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.153 — Ntn hydrolase-like
超家族 Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
家族 Family family	d.153.1.1 — Class II glutamine amidotransferases

结构域编号 domain_id	d1gph21
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	d1gph22
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.153 — Ntn hydrolase-like
超家族 Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
家族 Family family	d.153.1.1 — Class II glutamine amidotransferases

结构域编号 domain_id	d1gph31
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	d1gph32
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.153 — Ntn hydrolase-like
超家族 Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
家族 Family family	d.153.1.1 — Class II glutamine amidotransferases

结构域编号 domain_id	d1gph41
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	d1gph42
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.153 — Ntn hydrolase-like
超家族 Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
家族 Family family	d.153.1.1 — Class II glutamine amidotransferases

CATH v4.4 (8 domains)

结构域编号 domain_id	1gph101
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain

结构域编号 domain_id	1gph102
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	1gph201
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain

结构域编号 domain_id	1gph202
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	1gph301
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain

结构域编号 domain_id	1gph302
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	1gph401
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain

结构域编号 domain_id	1gph402
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	158.800 Å
晶胞边长 b length_b	75.700 Å
晶胞边长 c length_c	94.100 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	91.40 °
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	3.000 Å
最低分辨率 resolution_low	7.000 Å
R 因子 r_factor	0.1820
R_work r_work	0.1820
R_free r_free	—

fit	/app/data/saxs_computation/gp/1gph/1gph.fit
pddf	/app/data/pr_computation/gp/1gph/1gph.pr.out
profile	/app/data/saxs_computation/gp/1gph/1gph.dat