1t8r

Crystal Structure of E. coli AMP Nucleosidase

Method: X-RAY DIFFRACTION D_max: 126.5 Å Quality: REASONABLE

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

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1t8r
沉积日期 deposition_date	2004-05-13
结构标题 title	Crystal Structure of E. coli AMP Nucleosidase
关键词 keywords	ALPHA-BETA-ALPHA SANDWICH, ALPHA-BETA FOLD, HYDROLASE; HYDROLASE
实验方法 method	X-RAY DIFFRACTION

▼

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

回转半径 Rg (Guinier) rg_guinier	42.52 Å
回转半径 Rg (电子) rg_electron	41.62 Å
零角强度 I(0) i0	1426150000.00
分子量 molecular_weight	311950.0 kDa
排除体积 excluded_volume	389210 Å³
包络体积 envelope_volume	504100 Å³
水化壳体积 shell_volume	92930 Å³
包络直径 envelope_diameter	130.8 Å
壳层 Rg shell_rg	53.12 Å
包络 Rg envelope_rg	40.86 Å
形状 Rg shape_rg	41.62 Å
总 Rg total_rg	42.05 Å
总原子数 total_atoms	21972
残基数 n_residues	2754
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

▼

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

最大尺寸 Dmax dmax	126.5 Å
Rg (实空间) rg_real	42.19 Å
Rg 误差 (实空间) rg_real_error	0.61 Å
I(0) (实空间) i0_real	1.4260e+09
I(0) 误差 (实空间) i0_real_error	2.1780e+07
Rg (倒空间) rg_reciprocal	42.52 Å
I(0) (倒空间) i0_reciprocal	1427000000.0000
解质量估计 total_estimate	0.6873
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	58.1 Å
偏度 Skewness skewness	-0.030
峰度 Kurtosis kurtosis	-0.599
角度范围 angular_range	— – 0.1850 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	360000000.0000
实空间数据点数 n_real_points	38
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.927; Stabil: 1.000; Sysdev: 0.083; Positv: 1.000; Valcen: 0.952; Smooth: 0.948

▶

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

▶

5. 实体与聚合体信息 (2)

Entity 1 polymer

描述 description	AMP nucleosidase
分子量 formula_weight	54244.3 kDa
EC 编号 ec_number	3.2.2.4
来源方法 src_method	man
拷贝数 entity_count	6

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F
原子数 atom_count	22181

MNNKGSGLTPAQALDKLDALYEQSVVALRNAIGNYITSGELPDENARKQGLFVYPSLTVTWDGSTTNPPKTRAFGRFTHAGSYTTTITRPTLFRSYLNEQLTLLYQDYGAHISVQPSQHEIPYPYVIDGSELTLDRSMSAGLTRYFPTTELAQIGDETADGIYHPTEFSPLSHFDARRVDFSLARLRHYTGTPVEHFQPFVLFTNYTRYVDEFVRWGCSQILDPDSPYIALSCAGGNWITAETEAPEEAISDLAWKKHQMPAWHLITADGQGITLVNIGVGPSNAKTICDHLAVLRPDVWLMIGHCGGLRESQAIGDYVLAHAYLRDDHVLDAVLPPDIPIPSIAEVQRALYDATKLVSGRPGEEVKQRLRTGTVVTTDDRNWELRYSASALRFNLSRAVAIDMESATIAAQGYRFRVPYGTLLCVSDKPLHGEIKLPGQANRFYEGAISEHLQIGIRAIDLLRAEGDRLHSRKLRTFNEPPFR

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 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	209

▼

6. 折叠分类 (SCOP + CATH) 18 domains

SCOP 2.08 (6 domains)

结构域编号 domain_id	d1t8ra_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.56 — Phosphorylase/hydrolase-like
超家族 Superfamily superfamily	c.56.2 — Purine and uridine phosphorylases
家族 Family family	c.56.2.1 — Purine and uridine phosphorylases

结构域编号 domain_id	d1t8rb_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.56 — Phosphorylase/hydrolase-like
超家族 Superfamily superfamily	c.56.2 — Purine and uridine phosphorylases
家族 Family family	c.56.2.1 — Purine and uridine phosphorylases

结构域编号 domain_id	d1t8rc_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.56 — Phosphorylase/hydrolase-like
超家族 Superfamily superfamily	c.56.2 — Purine and uridine phosphorylases
家族 Family family	c.56.2.1 — Purine and uridine phosphorylases

结构域编号 domain_id	d1t8rd_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.56 — Phosphorylase/hydrolase-like
超家族 Superfamily superfamily	c.56.2 — Purine and uridine phosphorylases
家族 Family family	c.56.2.1 — Purine and uridine phosphorylases

结构域编号 domain_id	d1t8re_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.56 — Phosphorylase/hydrolase-like
超家族 Superfamily superfamily	c.56.2 — Purine and uridine phosphorylases
家族 Family family	c.56.2.1 — Purine and uridine phosphorylases

结构域编号 domain_id	d1t8rf_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.56 — Phosphorylase/hydrolase-like
超家族 Superfamily superfamily	c.56.2 — Purine and uridine phosphorylases
家族 Family family	c.56.2.1 — Purine and uridine phosphorylases

CATH v4.4 (12 domains)

结构域编号 domain_id	1t8rA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1730 — amp nucleosidase, domain 1
同源超家族 H-superfamily homologous superfamily	10 — AMP nucleoside phosphorylase, N-terminal domain

结构域编号 domain_id	1t8rA02
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	1580 — Nucleoside phosphorylase domain

结构域编号 domain_id	1t8rB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1730 — amp nucleosidase, domain 1
同源超家族 H-superfamily homologous superfamily	10 — AMP nucleoside phosphorylase, N-terminal domain

结构域编号 domain_id	1t8rB02
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	1580 — Nucleoside phosphorylase domain

结构域编号 domain_id	1t8rC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1730 — amp nucleosidase, domain 1
同源超家族 H-superfamily homologous superfamily	10 — AMP nucleoside phosphorylase, N-terminal domain

结构域编号 domain_id	1t8rC02
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	1580 — Nucleoside phosphorylase domain

结构域编号 domain_id	1t8rD01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1730 — amp nucleosidase, domain 1
同源超家族 H-superfamily homologous superfamily	10 — AMP nucleoside phosphorylase, N-terminal domain

结构域编号 domain_id	1t8rD02
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	1580 — Nucleoside phosphorylase domain

结构域编号 domain_id	1t8rE01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1730 — amp nucleosidase, domain 1
同源超家族 H-superfamily homologous superfamily	10 — AMP nucleoside phosphorylase, N-terminal domain

结构域编号 domain_id	1t8rE02
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	1580 — Nucleoside phosphorylase domain

结构域编号 domain_id	1t8rF01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1730 — amp nucleosidase, domain 1
同源超家族 H-superfamily homologous superfamily	10 — AMP nucleoside phosphorylase, N-terminal domain

结构域编号 domain_id	1t8rF02
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	1580 — Nucleoside phosphorylase domain

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	246.630 Å
晶胞边长 b length_b	246.630 Å
晶胞边长 c length_c	111.980 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	48

空间群 space_group	P 42 21 2
空间群编号 int_tables_number	94
晶系 crystal_system	—

分辨率 resolution	2.700 Å
最低分辨率 resolution_low	25.220 Å
R 因子 r_factor	0.2190
R_work r_work	0.2190
R_free r_free	0.2460

fit	/app/data/saxs_computation/t8/1t8r/1t8r.fit
pddf	/app/data/pr_computation/t8/1t8r/1t8r.pr.out
profile	/app/data/saxs_computation/t8/1t8r/1t8r.dat

Crystal Structure of E. coli AMP Nucleosidase

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