1g23

;THE STRUCTURAL BASIS OF THE CATALYTIC MECHANISM AND REGULATION OF GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE (RMLA). GLUCOSE-1-PHOSPHATE COMPLEX. ;

Method: X-RAY DIFFRACTION D_max: 169.1 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	1g23
沉积日期 deposition_date	2000-10-16
结构标题 title	;THE STRUCTURAL BASIS OF THE CATALYTIC MECHANISM AND REGULATION OF GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE (RMLA). GLUCOSE-1-PHOSPHATE COMPLEX. ;
关键词 keywords	L-rhamnose, nucleotidyltransferase, pyrophosphorylase, thymidylyltransferase, allostery, 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	49.48 Å
回转半径 Rg (电子) rg_electron	49.54 Å
零角强度 I(0) i0	985637000.00
分子量 molecular_weight	263020.0 kDa
排除体积 excluded_volume	329380 Å³
包络体积 envelope_volume	438410 Å³
水化壳体积 shell_volume	74375 Å³
包络直径 envelope_diameter	168.4 Å
壳层 Rg shell_rg	52.66 Å
包络 Rg envelope_rg	48.40 Å
形状 Rg shape_rg	49.55 Å
总 Rg total_rg	49.63 Å
总原子数 total_atoms	18473
残基数 n_residues	2312
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	169.1 Å
Rg (实空间) rg_real	49.79 Å
Rg 误差 (实空间) rg_real_error	1.90 Å
I(0) (实空间) i0_real	9.8560e+08
I(0) 误差 (实空间) i0_real_error	1.9850e+07
Rg (倒空间) rg_reciprocal	49.48 Å
I(0) (倒空间) i0_reciprocal	985200000.0000
解质量估计 total_estimate	0.8487
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	47.6 Å
偏度 Skewness skewness	0.414
峰度 Kurtosis kurtosis	-0.565
角度范围 angular_range	— – 0.1600 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	93860000.0000
实空间数据点数 n_real_points	33
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.769; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.936; Smooth: 0.785

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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	GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
分子量 formula_weight	32676.4 kDa
EC 编号 ec_number	2.7.7.24
来源方法 src_method	man
拷贝数 entity_count	8

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F,G,H
原子数 atom_count	18473

MKRKGIILAGGSGTRLHPATLAISKQLLPVYDKPMIYYPLSTLMLAGIREILIISTPQDTPRFQQLLGDGSNWGLDLQYAVQPSPDGLAQAFLIGESFIGNDLSALVLGDNLYYGHDFHELLGSASQRQTGASVFAYHVLDPERYGVVEFDQGGKAISLEEKPLEPKSNYAVTGLYFYDQQVVDIARDLKPSPRGELEITDVNRAYLERGQLSVEIMGRGYAWLDTGTHDSLLEAGQFIATLENRQGLKVACPEEIAYRQKWIDAAQLEKLAAPLAKNGYGQYLKRLLTETVY

来源 Source

来源生物 organism	Pseudomonas aeruginosa
NCBI 分类编号 ncbi_taxonomy_id	287
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	1-O-phosphono-alpha-D-glucopyranose
分子量 formula_weight	260.1 kDa
来源方法 src_method	man
拷贝数 entity_count	8

Entity 3 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	13

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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	d1g23a_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.68 — Nucleotide-diphospho-sugar transferases
超家族 Superfamily superfamily	c.68.1 — Nucleotide-diphospho-sugar transferases
家族 Family family	c.68.1.6 — glucose-1-phosphate thymidylyltransferase

结构域编号 domain_id	d1g23b_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.68 — Nucleotide-diphospho-sugar transferases
超家族 Superfamily superfamily	c.68.1 — Nucleotide-diphospho-sugar transferases
家族 Family family	c.68.1.6 — glucose-1-phosphate thymidylyltransferase

结构域编号 domain_id	d1g23c_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.68 — Nucleotide-diphospho-sugar transferases
超家族 Superfamily superfamily	c.68.1 — Nucleotide-diphospho-sugar transferases
家族 Family family	c.68.1.6 — glucose-1-phosphate thymidylyltransferase

结构域编号 domain_id	d1g23d_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.68 — Nucleotide-diphospho-sugar transferases
超家族 Superfamily superfamily	c.68.1 — Nucleotide-diphospho-sugar transferases
家族 Family family	c.68.1.6 — glucose-1-phosphate thymidylyltransferase

结构域编号 domain_id	d1g23e_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.68 — Nucleotide-diphospho-sugar transferases
超家族 Superfamily superfamily	c.68.1 — Nucleotide-diphospho-sugar transferases
家族 Family family	c.68.1.6 — glucose-1-phosphate thymidylyltransferase

结构域编号 domain_id	d1g23f_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.68 — Nucleotide-diphospho-sugar transferases
超家族 Superfamily superfamily	c.68.1 — Nucleotide-diphospho-sugar transferases
家族 Family family	c.68.1.6 — glucose-1-phosphate thymidylyltransferase

结构域编号 domain_id	d1g23g_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.68 — Nucleotide-diphospho-sugar transferases
超家族 Superfamily superfamily	c.68.1 — Nucleotide-diphospho-sugar transferases
家族 Family family	c.68.1.6 — glucose-1-phosphate thymidylyltransferase

结构域编号 domain_id	d1g23h_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.68 — Nucleotide-diphospho-sugar transferases
超家族 Superfamily superfamily	c.68.1 — Nucleotide-diphospho-sugar transferases
家族 Family family	c.68.1.6 — glucose-1-phosphate thymidylyltransferase

CATH v4.4 (8 domains)

结构域编号 domain_id	1g23A00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	550 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A

结构域编号 domain_id	1g23B00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	550 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A

结构域编号 domain_id	1g23C00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	550 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A

结构域编号 domain_id	1g23D00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	550 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A

结构域编号 domain_id	1g23E00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	550 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A

结构域编号 domain_id	1g23F00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	550 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A

结构域编号 domain_id	1g23G00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	550 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A

结构域编号 domain_id	1g23H00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	550 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A

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7. 引用文献 (3)

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晶胞边长 a length_a	71.583 Å
晶胞边长 b length_b	73.901 Å
晶胞边长 c length_c	133.748 Å
晶胞夹角 α angle_alpha	89.81 °
晶胞夹角 β angle_beta	80.31 °
晶胞夹角 γ angle_gamma	80.18 °
晶胞分子数 Z z_pdb	8

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

分辨率 resolution	2.800 Å
最低分辨率 resolution_low	72.550 Å
R 因子 r_factor	0.2011
R_work r_work	0.1990
R_free r_free	0.2260

fit	/app/data/saxs_computation/g2/1g23/1g23.fit
pddf	/app/data/pr_computation/g2/1g23/1g23.pr.out
profile	/app/data/saxs_computation/g2/1g23/1g23.dat