2ggk

The mutant A302C of Agrobacterium radiobacter N-carbamoyl-D-amino-acid amidohydrolase

Method: X-RAY DIFFRACTION D_max: 91.2 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	2ggk
沉积日期 deposition_date	2006-03-24
结构标题 title	The mutant A302C of Agrobacterium radiobacter N-carbamoyl-D-amino-acid amidohydrolase
关键词 keywords	N-Carbamoyl-D-Amino-Acid Amidohydrolase, 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	30.95 Å
回转半径 Rg (电子) rg_electron	30.11 Å
零角强度 I(0) i0	285798000.00
分子量 molecular_weight	135770.0 kDa
排除体积 excluded_volume	169800 Å³
包络体积 envelope_volume	194570 Å³
水化壳体积 shell_volume	50952 Å³
包络直径 envelope_diameter	99.6 Å
壳层 Rg shell_rg	39.41 Å
包络 Rg envelope_rg	30.27 Å
形状 Rg shape_rg	30.12 Å
总 Rg total_rg	30.80 Å
总原子数 total_atoms	9568
残基数 n_residues	1208
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	91.2 Å
Rg (实空间) rg_real	30.71 Å
Rg 误差 (实空间) rg_real_error	0.51 Å
I(0) (实空间) i0_real	2.8580e+08
I(0) 误差 (实空间) i0_real_error	3.7200e+06
Rg (倒空间) rg_reciprocal	30.82 Å
I(0) (倒空间) i0_reciprocal	285800000.0000
解质量估计 total_estimate	0.6741
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	41.1 Å
偏度 Skewness skewness	0.073
峰度 Kurtosis kurtosis	-0.581
角度范围 angular_range	— – 0.2550 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	189100000.0000
实空间数据点数 n_real_points	52
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.959; Stabil: 0.999; Sysdev: 0.040; Positv: 1.000; Valcen: 0.977; Smooth: 0.790

▶

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

▶

5. 实体与聚合体信息 (2)

▼

6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d2ggka1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.160 — Carbon-nitrogen hydrolase
超家族 Superfamily superfamily	d.160.1 — Carbon-nitrogen hydrolase
家族 Family family	d.160.1.2 — Carbamilase

结构域编号 domain_id	d2ggkb_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.160 — Carbon-nitrogen hydrolase
超家族 Superfamily superfamily	d.160.1 — Carbon-nitrogen hydrolase
家族 Family family	d.160.1.2 — Carbamilase

结构域编号 domain_id	d2ggkc_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.160 — Carbon-nitrogen hydrolase
超家族 Superfamily superfamily	d.160.1 — Carbon-nitrogen hydrolase
家族 Family family	d.160.1.2 — Carbamilase

结构域编号 domain_id	d2ggkd_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.160 — Carbon-nitrogen hydrolase
超家族 Superfamily superfamily	d.160.1 — Carbon-nitrogen hydrolase
家族 Family family	d.160.1.2 — Carbamilase

CATH v4.4 (4 domains)

结构域编号 domain_id	2ggkA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	110 — Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase
同源超家族 H-superfamily homologous superfamily	10 — Carbon-nitrogen hydrolase

结构域编号 domain_id	2ggkB00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	110 — Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase
同源超家族 H-superfamily homologous superfamily	10 — Carbon-nitrogen hydrolase

结构域编号 domain_id	2ggkC00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	110 — Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase
同源超家族 H-superfamily homologous superfamily	10 — Carbon-nitrogen hydrolase

结构域编号 domain_id	2ggkD00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	110 — Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase
同源超家族 H-superfamily homologous superfamily	10 — Carbon-nitrogen hydrolase

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	69.091 Å
晶胞边长 b length_b	67.819 Å
晶胞边长 c length_c	138.037 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	95.87 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

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	2.300 Å
最低分辨率 resolution_low	30.000 Å
R 因子 r_factor	0.1802
R_work r_work	0.1782
R_free r_free	0.2196

描述 description	N-carbamoyl-D-amino acid amidohydrolase
分子量 formula_weight	34241.1 kDa
EC 编号 ec_number	3.5.1.77
突变 mutation	A302C
来源方法 src_method	man
拷贝数 entity_count	4

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	9853

The mutant A302C of Agrobacterium radiobacter N-carbamoyl-D-amino-acid amidohydrolase

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 (2)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 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)

来源生物 organism	Agrobacterium tumefaciens
NCBI 分类编号 ncbi_taxonomy_id	358
宿主生物 host_organism	Escherichia coli

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	285

fit	/app/data/saxs_computation/gg/2ggk/2ggk.fit
pddf	/app/data/pr_computation/gg/2ggk/2ggk.pr.out
profile	/app/data/saxs_computation/gg/2ggk/2ggk.dat