SAXSdb — 1h5r

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1h5r
沉积日期 deposition_date	2001-05-25
结构标题 title	Thymidylyltransferase complexed with Thimidine and Glucose-1-phospate
关键词 keywords	TRANSFERASE, PYROPHOSPHATASE, NUCLEOTIDE SUGAR METHABOLISM; 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	32.17 Å
回转半径 Rg (电子) rg_electron	30.97 Å
零角强度 I(0) i0	266060000.00
分子量 molecular_weight	132560.0 kDa
排除体积 excluded_volume	166760 Å³
包络体积 envelope_volume	199940 Å³
水化壳体积 shell_volume	50967 Å³
包络直径 envelope_diameter	98.5 Å
壳层 Rg shell_rg	40.05 Å
包络 Rg envelope_rg	30.92 Å
形状 Rg shape_rg	30.94 Å
总 Rg total_rg	31.79 Å
总原子数 total_atoms	9318
残基数 n_residues	1160
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	97.3 Å
Rg (实空间) rg_real	31.92 Å
Rg 误差 (实空间) rg_real_error	0.46 Å
I(0) (实空间) i0_real	2.6610e+08
I(0) 误差 (实空间) i0_real_error	3.9260e+06
Rg (倒空间) rg_reciprocal	32.03 Å
I(0) (倒空间) i0_reciprocal	266100000.0000
解质量估计 total_estimate	0.6561
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	41.7 Å
偏度 Skewness skewness	0.076
峰度 Kurtosis kurtosis	-0.572
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	121500000.0000
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: 0.941; Stabil: 1.000; Sysdev: 0.242; Positv: 1.000; Valcen: 0.976; Smooth: 0.000

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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 (6)

Entity 1 polymer

描述 description	GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
分子量 formula_weight	32726.5 kDa
EC 编号 ec_number	2.7.7.24
来源方法 src_method	man
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,C,D
原子数 atom_count	9791

MKMRKGIILAGGSGTRLYPVTMAVSKQLLPIYDKPMIYYPLSTLMLAGIRDILIISTPQDTPRFQQLLGDGSQWGLNLQYKVQPSPDGLAQAFIIGEEFIGGDDCALVLGDNIFYGHDLPKLMEAAVNKESGATVFAYHVNDPERYGVVEFDKNGTAISLEEKPLEPKSNYAVTGLYFYDNDVVQMAKNLKPSARGELEITDINRIYLEQGRLSVAMMGRGYAWLDTGTHQSLIEASNFIATIEERQGLKVSCPEEIAFRKGFIDVEQVRKLAVPLIKNNYGQYLYKMTKDSN

来源 Source

来源生物 organism	ESCHERICHIA COLI
NCBI 分类编号 ncbi_taxonomy_id	562
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 polymer

描述 description	GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
分子量 formula_weight	32705.4 kDa
EC 编号 ec_number	2.7.7.24
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B

MKMRKGIILAGGSGTRLYPVTMAVSKQLLPIYDKPMIYYPLSTLMLAGIRDILIISTPQDTPRFQQLLGDGSQWGLNLQYKVQPSPDGLAQAFIIGEEFIGGDDCALVLGDNIFYGHDLPKLMEAAVNKESGATVFAYHVNDPERYGVVEFDKNGTAISLEEKPLEPKSNYAVTGLYFYDNDVVQMAKNLKPSARGELEITDINRIYLEQGRLSVALMGRGYAWLDTGTHQSLIEASNFIATIEERQGLKVSCPEEIAFRKGFIDVEQVRKLAVPLIKNNYGQYLYKQTKDSN

来源 Source

来源生物 organism	ESCHERICHIA COLI
NCBI 分类编号 ncbi_taxonomy_id	562
宿主生物 host_organism	ESCHERICHIA COLI

Entity 3 non-polymer

描述 description	THYMIDINE
分子量 formula_weight	242.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	8

Entity 4 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	4

Entity 5 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 6 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	473

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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	d1h5ra_
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	d1h5rb_
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	d1h5rc_
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	d1h5rd_
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	1h5rA00
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	1h5rB00
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	1h5rC00
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	1h5rD00
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 (1)

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晶胞边长 a length_a	72.810 Å
晶胞边长 b length_b	118.960 Å
晶胞边长 c length_c	80.590 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	112.60 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	6

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	1.900 Å
最低分辨率 resolution_low	12.000 Å
R 因子 r_factor	—
R_work r_work	0.1730
R_free r_free	0.2340

fit	/app/data/saxs_computation/h5/1h5r/1h5r.fit
pddf	/app/data/pr_computation/h5/1h5r/1h5r.pr.out
profile	/app/data/saxs_computation/h5/1h5r/1h5r.dat

Thymidylyltransferase complexed with Thimidine and Glucose-1-phospate

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

5. 实体与聚合体信息 (6)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 water

6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)