SAXSdb — 2j4r

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2j4r
沉积日期 deposition_date	2006-09-05
结构标题 title	Structural Study of the Aquifex aeolicus PPX-GPPA enzyme
关键词 keywords	PPGPP, AQUIFEX AEOLICUS, STRINGENT RESPONSE, HYDROLASE, EXOPOLYPHOSPHATASE, GUANOSINE PENTAPHOSPHATE; 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	28.52 Å
回转半径 Rg (电子) rg_electron	27.63 Å
零角强度 I(0) i0	70912600.00
分子量 molecular_weight	68502.0 kDa
排除体积 excluded_volume	87047 Å³
包络体积 envelope_volume	107380 Å³
水化壳体积 shell_volume	32924 Å³
包络直径 envelope_diameter	97.4 Å
壳层 Rg shell_rg	34.53 Å
包络 Rg envelope_rg	27.53 Å
形状 Rg shape_rg	27.60 Å
总 Rg total_rg	28.46 Å
总原子数 total_atoms	4828
残基数 n_residues	600
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	92.7 Å
Rg (实空间) rg_real	28.54 Å
Rg 误差 (实空间) rg_real_error	0.56 Å
I(0) (实空间) i0_real	7.0910e+07
I(0) 误差 (实空间) i0_real_error	9.7910e+05
Rg (倒空间) rg_reciprocal	28.54 Å
I(0) (倒空间) i0_reciprocal	70910000.0000
解质量估计 total_estimate	0.8915
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	31.4 Å
偏度 Skewness skewness	0.361
峰度 Kurtosis kurtosis	-0.365
角度范围 angular_range	— – 0.2800 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	16270000.0000
实空间数据点数 n_real_points	57
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.898; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.907

▶

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

▶

5. 实体与聚合体信息 (3)

Entity 1 polymer

描述 description	EXOPOLYPHOSPHATASE
分子量 formula_weight	34998.4 kDa
突变 mutation	YES
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	4997

GSHMPIMRVASIDIGSNSVRLTIAQIKDGKLSIILERGRITSLGTKVKETGRLQEDRIEETIQVLKEYKKLIDEFKVERVKAVATEAIRRAKNAEEFLERVKREVGLVVEVITPEQEGRYAYLAVAYSLKPEGEVCVVDQGGGSTEYVFGKGYKVREVISLPIGIVNLTETFFKQDPPTEEEVKRFFEFLEKELSKVKKPVDTIVGLGGTITTLAALEYNVYPYDPQKVHGKVLTYGQIKKWFDTFKEIPSEERSKRFRQVEDRRAKVILAGIGIFLKTLEIFEKDCLIVSDWGLREGVLVSEVLKEN

来源 Source

来源生物 organism	AQUIFEX AEOLICUS
NCBI 分类编号 ncbi_taxonomy_id	63363
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 non-polymer

描述 description	GUANOSINE-5',3'-TETRAPHOSPHATE
分子量 formula_weight	603.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 3 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

▼

6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d2j4ra1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.55 — Ribonuclease H-like motif
超家族 Superfamily superfamily	c.55.1 — Actin-like ATPase domain
家族 Family family	c.55.1.8 — Ppx/GppA phosphatase

结构域编号 domain_id	d2j4ra2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.55 — Ribonuclease H-like motif
超家族 Superfamily superfamily	c.55.1 — Actin-like ATPase domain
家族 Family family	c.55.1.8 — Ppx/GppA phosphatase

结构域编号 domain_id	d2j4rb1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.55 — Ribonuclease H-like motif
超家族 Superfamily superfamily	c.55.1 — Actin-like ATPase domain
家族 Family family	c.55.1.8 — Ppx/GppA phosphatase

结构域编号 domain_id	d2j4rb2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.55 — Ribonuclease H-like motif
超家族 Superfamily superfamily	c.55.1 — Actin-like ATPase domain
家族 Family family	c.55.1.8 — Ppx/GppA phosphatase

CATH v4.4 (4 domains)

结构域编号 domain_id	2j4rA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	420 — Nucleotidyltransferase; domain 5
同源超家族 H-superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

结构域编号 domain_id	2j4rA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	420 — Nucleotidyltransferase; domain 5
同源超家族 H-superfamily homologous superfamily	150 — Exopolyphosphatase. Domain 2

结构域编号 domain_id	2j4rB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	420 — Nucleotidyltransferase; domain 5
同源超家族 H-superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

结构域编号 domain_id	2j4rB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	420 — Nucleotidyltransferase; domain 5
同源超家族 H-superfamily homologous superfamily	150 — Exopolyphosphatase. Domain 2

▶

7. 引用文献 (2)

▶

晶胞边长 a length_a	70.460 Å
晶胞边长 b length_b	70.460 Å
晶胞边长 c length_c	223.710 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	120.00 °
晶胞分子数 Z z_pdb	12

空间群 space_group	P 32 2 1
空间群编号 int_tables_number	154
晶系 crystal_system	—

分辨率 resolution	2.710 Å
最低分辨率 resolution_low	61.020 Å
R 因子 r_factor	0.2120
R_work r_work	0.2120
R_free r_free	0.2960

fit	/app/data/saxs_computation/j4/2j4r/2j4r.fit
pddf	/app/data/pr_computation/j4/2j4r/2j4r.pr.out
profile	/app/data/saxs_computation/j4/2j4r/2j4r.dat

Structural Study of the Aquifex aeolicus PPX-GPPA enzyme

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