SAXSdb — 1g3l

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1g3l
沉积日期 deposition_date	2000-10-24
结构标题 title	;THE STRUCTURAL BASIS OF THE CATALYTIC MECHANISM AND REGULATION OF GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE (RMLA). TDP-L-RHAMNOSE 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	32.15 Å
回转半径 Rg (电子) rg_electron	30.91 Å
零角强度 I(0) i0	280474000.00
分子量 molecular_weight	134270.0 kDa
排除体积 excluded_volume	167990 Å³
包络体积 envelope_volume	201060 Å³
水化壳体积 shell_volume	51131 Å³
包络直径 envelope_diameter	99.9 Å
壳层 Rg shell_rg	40.21 Å
包络 Rg envelope_rg	30.95 Å
形状 Rg shape_rg	30.90 Å
总 Rg total_rg	31.70 Å
总原子数 total_atoms	9453
残基数 n_residues	1169
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	97.4 Å
Rg (实空间) rg_real	31.90 Å
Rg 误差 (实空间) rg_real_error	0.42 Å
I(0) (实空间) i0_real	2.8050e+08
I(0) 误差 (实空间) i0_real_error	3.4880e+06
Rg (倒空间) rg_reciprocal	32.01 Å
I(0) (倒空间) i0_reciprocal	280500000.0000
解质量估计 total_estimate	0.9047
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	41.7 Å
偏度 Skewness skewness	0.081
峰度 Kurtosis kurtosis	-0.575
角度范围 angular_range	— – 0.2450 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	144000000.0000
实空间数据点数 n_real_points	50
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.940; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.976; Smooth: 0.959

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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	32488.8 kDa
EC 编号 ec_number	2.7.7.24
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	9453

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	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	5

Entity 3 non-polymer

描述 description	2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE
分子量 formula_weight	548.3 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) 8 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1g3la_
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	d1g3lb_
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	d1g3lc_
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	d1g3ld_
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 (4 domains)

结构域编号 domain_id	1g3lA00
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	1g3lB00
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	1g3lC00
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	1g3lD00
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	71.087 Å
晶胞边长 b length_b	138.557 Å
晶胞边长 c length_c	139.676 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	90.00 °
晶胞分子数 Z z_pdb	16

空间群 space_group	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	2.700 Å
最低分辨率 resolution_low	100.000 Å
R 因子 r_factor	0.2050
R_work r_work	0.2040
R_free r_free	0.2300

fit	/app/data/saxs_computation/g3/1g3l/1g3l.fit
pddf	/app/data/pr_computation/g3/1g3l/1g3l.pr.out
profile	/app/data/saxs_computation/g3/1g3l/1g3l.dat

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

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

1. 结构基本信息 1. Structure Basics

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

4. 晶体学与实验 4. Crystallography & Experiment

晶胞参数 Unit Cell

对称性 Symmetry

精修参数 Refinement

衍射实验 Diffraction