2jer

Agmatine deiminase of Enterococcus faecalis catalyzing its reaction.

Method: X-RAY DIFFRACTION D_max: 167.9 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	2jer
沉积日期 deposition_date	2007-01-19
结构标题 title	Agmatine deiminase of Enterococcus faecalis catalyzing its reaction.
关键词 keywords	;HYDROLASE, AGMATINE DEIMINASE, TETRAMER, AGDI, 5- FOLD PSEUDOSYMMETRIC STRUCTURE, AGMATINE DEGRADATION PATHWAY, COVALENT AMIDINO ADDUCT, AGMATINE IMINOHYDROLASE ;; 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	48.71 Å
回转半径 Rg (电子) rg_electron	48.78 Å
零角强度 I(0) i0	1642640000.00
分子量 molecular_weight	330600.0 kDa
排除体积 excluded_volume	409940 Å³
包络体积 envelope_volume	521030 Å³
水化壳体积 shell_volume	87742 Å³
包络直径 envelope_diameter	178.1 Å
壳层 Rg shell_rg	53.93 Å
包络 Rg envelope_rg	48.13 Å
形状 Rg shape_rg	48.76 Å
总 Rg total_rg	49.03 Å
总原子数 total_atoms	23234
残基数 n_residues	2927
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	167.9 Å
Rg (实空间) rg_real	48.84 Å
Rg 误差 (实空间) rg_real_error	1.54 Å
I(0) (实空间) i0_real	1.6430e+09
I(0) 误差 (实空间) i0_real_error	3.2730e+07
Rg (倒空间) rg_reciprocal	48.71 Å
I(0) (倒空间) i0_reciprocal	1642000000.0000
解质量估计 total_estimate	0.6315
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	57.7 Å
偏度 Skewness skewness	0.437
峰度 Kurtosis kurtosis	-0.180
角度范围 angular_range	— – 0.1600 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	113300000.0000
实空间数据点数 n_real_points	33
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.792; Stabil: 1.000; Sysdev: 0.013; Positv: 1.000; Valcen: 0.995; Smooth: 0.796

▶

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) 17 domains

SCOP 2.08 (9 domains)

结构域编号 domain_id	d2jera1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.126 — Pentein, beta/alpha-propeller
超家族 Superfamily superfamily	d.126.1 — Pentein
家族 Family family	d.126.1.6 — Porphyromonas-type peptidylarginine deiminase

结构域编号 domain_id	d2jerb_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.126 — Pentein, beta/alpha-propeller
超家族 Superfamily superfamily	d.126.1 — Pentein
家族 Family family	d.126.1.6 — Porphyromonas-type peptidylarginine deiminase

结构域编号 domain_id	d2jerc_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.126 — Pentein, beta/alpha-propeller
超家族 Superfamily superfamily	d.126.1 — Pentein
家族 Family family	d.126.1.6 — Porphyromonas-type peptidylarginine deiminase

结构域编号 domain_id	d2jerd2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.126 — Pentein, beta/alpha-propeller
超家族 Superfamily superfamily	d.126.1 — Pentein
家族 Family family	d.126.1.6 — Porphyromonas-type peptidylarginine deiminase

结构域编号 domain_id	d2jerd3
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d2jere_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.126 — Pentein, beta/alpha-propeller
超家族 Superfamily superfamily	d.126.1 — Pentein
家族 Family family	d.126.1.6 — Porphyromonas-type peptidylarginine deiminase

结构域编号 domain_id	d2jerf_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.126 — Pentein, beta/alpha-propeller
超家族 Superfamily superfamily	d.126.1 — Pentein
家族 Family family	d.126.1.6 — Porphyromonas-type peptidylarginine deiminase

结构域编号 domain_id	d2jerg_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.126 — Pentein, beta/alpha-propeller
超家族 Superfamily superfamily	d.126.1 — Pentein
家族 Family family	d.126.1.6 — Porphyromonas-type peptidylarginine deiminase

结构域编号 domain_id	d2jerh_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.126 — Pentein, beta/alpha-propeller
超家族 Superfamily superfamily	d.126.1 — Pentein
家族 Family family	d.126.1.6 — Porphyromonas-type peptidylarginine deiminase

CATH v4.4 (8 domains)

结构域编号 domain_id	2jerA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	75 — 5-stranded Propeller
拓扑 Topology topology	10 — L-arginine/glycine Amidinotransferase; Chain A
同源超家族 H-superfamily homologous superfamily	10 — L-arginine/glycine Amidinotransferase; Chain A

结构域编号 domain_id	2jerB00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	75 — 5-stranded Propeller
拓扑 Topology topology	10 — L-arginine/glycine Amidinotransferase; Chain A
同源超家族 H-superfamily homologous superfamily	10 — L-arginine/glycine Amidinotransferase; Chain A

结构域编号 domain_id	2jerC00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	75 — 5-stranded Propeller
拓扑 Topology topology	10 — L-arginine/glycine Amidinotransferase; Chain A
同源超家族 H-superfamily homologous superfamily	10 — L-arginine/glycine Amidinotransferase; Chain A

结构域编号 domain_id	2jerD00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	75 — 5-stranded Propeller
拓扑 Topology topology	10 — L-arginine/glycine Amidinotransferase; Chain A
同源超家族 H-superfamily homologous superfamily	10 — L-arginine/glycine Amidinotransferase; Chain A

结构域编号 domain_id	2jerE00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	75 — 5-stranded Propeller
拓扑 Topology topology	10 — L-arginine/glycine Amidinotransferase; Chain A
同源超家族 H-superfamily homologous superfamily	10 — L-arginine/glycine Amidinotransferase; Chain A

结构域编号 domain_id	2jerF00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	75 — 5-stranded Propeller
拓扑 Topology topology	10 — L-arginine/glycine Amidinotransferase; Chain A
同源超家族 H-superfamily homologous superfamily	10 — L-arginine/glycine Amidinotransferase; Chain A

结构域编号 domain_id	2jerG00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	75 — 5-stranded Propeller
拓扑 Topology topology	10 — L-arginine/glycine Amidinotransferase; Chain A
同源超家族 H-superfamily homologous superfamily	10 — L-arginine/glycine Amidinotransferase; Chain A

结构域编号 domain_id	2jerH00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	75 — 5-stranded Propeller
拓扑 Topology topology	10 — L-arginine/glycine Amidinotransferase; Chain A
同源超家族 H-superfamily homologous superfamily	10 — L-arginine/glycine Amidinotransferase; Chain A

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	107.727 Å
晶胞边长 b length_b	130.165 Å
晶胞边长 c length_c	126.726 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	93.61 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	16

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	1.650 Å
最低分辨率 resolution_low	50.000 Å
R 因子 r_factor	0.1680
R_work r_work	0.1670
R_free r_free	0.1920

描述 description	AGMATINE DEIMINASE
分子量 formula_weight	43960.3 kDa
EC 编号 ec_number	3.5.3.12
来源方法 src_method	man
拷贝数 entity_count	8

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F,G,H
原子数 atom_count	25408

Agmatine deiminase of Enterococcus faecalis catalyzing its reaction.

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) 17 domains

SCOP 2.08 (9 domains)

CATH v4.4 (8 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)

来源生物 organism	ENTEROCOCCUS FAECALIS
NCBI 分类编号 ncbi_taxonomy_id	1351
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	2174

fit	/app/data/saxs_computation/je/2jer/2jer.fit
pddf	/app/data/pr_computation/je/2jer/2jer.pr.out
profile	/app/data/saxs_computation/je/2jer/2jer.dat