SAXSdb — 1n1d

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1n1d
沉积日期 deposition_date	2002-10-17
结构标题 title	Glycerol-3-phosphate cytidylyltransferase complexed with CDP-glycerol
关键词 keywords	alpha/beta fold, cytidylyltransferase, nucleotidyltransferase, negative cooperativity, CDP-glycerol, 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	30.27 Å
回转半径 Rg (电子) rg_electron	30.24 Å
零角强度 I(0) i0	60824200.00
分子量 molecular_weight	62234.0 kDa
排除体积 excluded_volume	78156 Å³
包络体积 envelope_volume	94437 Å³
水化壳体积 shell_volume	28087 Å³
包络直径 envelope_diameter	112.1 Å
壳层 Rg shell_rg	34.48 Å
包络 Rg envelope_rg	30.19 Å
形状 Rg shape_rg	30.23 Å
总 Rg total_rg	30.65 Å
总原子数 total_atoms	4379
残基数 n_residues	504
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	109.0 Å
Rg (实空间) rg_real	30.55 Å
Rg 误差 (实空间) rg_real_error	1.26 Å
I(0) (实空间) i0_real	6.0820e+07
I(0) 误差 (实空间) i0_real_error	9.9550e+05
Rg (倒空间) rg_reciprocal	30.43 Å
I(0) (倒空间) i0_reciprocal	60820000.0000
解质量估计 total_estimate	0.7991
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	25.2 Å
偏度 Skewness skewness	0.561
峰度 Kurtosis kurtosis	-0.130
角度范围 angular_range	— – 0.2600 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	29400000.0000
实空间数据点数 n_real_points	53
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.655; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.602; Smooth: 0.829

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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 (4)

Entity 1 polymer

描述 description	glycerol-3-phosphate cytidylyltransferase
分子量 formula_weight	15295.5 kDa
EC 编号 ec_number	2.7.7.39
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	4548

MKKVITYGTFDLLHWGHIKLLERAKQLGDYLVVAISTDEFNLQKQKKAYHSYEHRKLILETIRYVDEVIPEKNWEQKKQDIIDHNIDVFVMGDDWEGKFDFLKDQCEVVYLPRTEGISTTKIKEEIAGL

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	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 3 non-polymer

描述 description	;[CYTIDINE-5'-PHOSPHATE] GLYCERYLPHOSPHORIC ACID ESTER ;
分子量 formula_weight	477.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 4 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	169

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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	d1n1da_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.26 — Adenine nucleotide alpha hydrolase-like
超家族 Superfamily superfamily	c.26.1 — Nucleotidylyl transferase
家族 Family family	c.26.1.2 — Cytidylyltransferase

结构域编号 domain_id	d1n1db_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.26 — Adenine nucleotide alpha hydrolase-like
超家族 Superfamily superfamily	c.26.1 — Nucleotidylyl transferase
家族 Family family	c.26.1.2 — Cytidylyltransferase

结构域编号 domain_id	d1n1dc_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.26 — Adenine nucleotide alpha hydrolase-like
超家族 Superfamily superfamily	c.26.1 — Nucleotidylyl transferase
家族 Family family	c.26.1.2 — Cytidylyltransferase

结构域编号 domain_id	d1n1dd_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.26 — Adenine nucleotide alpha hydrolase-like
超家族 Superfamily superfamily	c.26.1 — Nucleotidylyl transferase
家族 Family family	c.26.1.2 — Cytidylyltransferase

CATH v4.4 (4 domains)

结构域编号 domain_id	1n1dA00
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	620 — HUPs

结构域编号 domain_id	1n1dB00
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	620 — HUPs

结构域编号 domain_id	1n1dC00
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	620 — HUPs

结构域编号 domain_id	1n1dD00
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	620 — HUPs

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7. 引用文献 (2)

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晶胞边长 a length_a	37.795 Å
晶胞边长 b length_b	55.929 Å
晶胞边长 c length_c	63.701 Å
晶胞夹角 α angle_alpha	88.99 °
晶胞夹角 β angle_beta	75.03 °
晶胞夹角 γ angle_gamma	82.54 °
晶胞分子数 Z z_pdb	4

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

分辨率 resolution	2.000 Å
最低分辨率 resolution_low	15.000 Å
R 因子 r_factor	0.2463
R_work r_work	0.2409
R_free r_free	0.2944

fit	/app/data/saxs_computation/n1/1n1d/1n1d.fit
pddf	/app/data/pr_computation/n1/1n1d/1n1d.pr.out
profile	/app/data/saxs_computation/n1/1n1d/1n1d.dat

Glycerol-3-phosphate cytidylyltransferase complexed with CDP-glycerol

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 (4)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 non-polymer

Entity 3 non-polymer

Entity 4 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 (2)

8. 文件与曲线 (10)

Files (7)

Curves (3)