1yvw

Crystal structure of Phosphoribosyl-ATP pyrophosphohydrolase from Bacillus cereus. NESGC target BcR13.

Method: X-RAY DIFFRACTION D_max: 65.3 Å Quality: EXCELLENT

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

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1yvw
沉积日期 deposition_date	2005-02-16
结构标题 title	Crystal structure of Phosphoribosyl-ATP pyrophosphohydrolase from Bacillus cereus. NESGC target BcR13.
关键词 keywords	;HELIX BUNDLE, HISTIDINE BIOSYNTHESIS, pyrophosphatase, Structural Genomics, PSI, Protein Structure Initiative, Northeast Structural Genomics Consortium, NESG, HYDROLASE ;; HYDROLASE
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	22.13 Å
回转半径 Rg (电子) rg_electron	21.12 Å
零角强度 I(0) i0	29742200.00
分子量 molecular_weight	43001.0 kDa
排除体积 excluded_volume	54239 Å³
包络体积 envelope_volume	61895 Å³
水化壳体积 shell_volume	24116 Å³
包络直径 envelope_diameter	65.5 Å
壳层 Rg shell_rg	28.03 Å
包络 Rg envelope_rg	21.35 Å
形状 Rg shape_rg	21.15 Å
总 Rg total_rg	21.91 Å
总原子数 total_atoms	2988
残基数 n_residues	360
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	65.3 Å
Rg (实空间) rg_real	22.00 Å
Rg 误差 (实空间) rg_real_error	0.34 Å
I(0) (实空间) i0_real	2.9740e+07
I(0) 误差 (实空间) i0_real_error	3.7500e+05
Rg (倒空间) rg_reciprocal	22.03 Å
I(0) (倒空间) i0_reciprocal	29740000.0000
解质量估计 total_estimate	0.9160
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	27.3 Å
偏度 Skewness skewness	0.172
峰度 Kurtosis kurtosis	-0.531
角度范围 angular_range	— – 0.3600 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	8468000.0000
实空间数据点数 n_real_points	68
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.973; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.990

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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 (2)

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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	d1yvwa1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.204 — all-alpha NTP pyrophosphatases
超家族 Superfamily superfamily	a.204.1 — all-alpha NTP pyrophosphatases
家族 Family family	a.204.1.4 — HisE-like (PRA-PH)

结构域编号 domain_id	d1yvwb_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.204 — all-alpha NTP pyrophosphatases
超家族 Superfamily superfamily	a.204.1 — all-alpha NTP pyrophosphatases
家族 Family family	a.204.1.4 — HisE-like (PRA-PH)

结构域编号 domain_id	d1yvwc_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.204 — all-alpha NTP pyrophosphatases
超家族 Superfamily superfamily	a.204.1 — all-alpha NTP pyrophosphatases
家族 Family family	a.204.1.4 — HisE-like (PRA-PH)

结构域编号 domain_id	d1yvwd_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.204 — all-alpha NTP pyrophosphatases
超家族 Superfamily superfamily	a.204.1 — all-alpha NTP pyrophosphatases
家族 Family family	a.204.1.4 — HisE-like (PRA-PH)

CATH v4.4 (4 domains)

结构域编号 domain_id	1yvwA00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily	1080 — MazG-like

结构域编号 domain_id	1yvwB00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily	1080 — MazG-like

结构域编号 domain_id	1yvwC00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily	1080 — MazG-like

结构域编号 domain_id	1yvwD00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily	1080 — MazG-like

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7. 引用文献 (1)

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晶胞边长 a length_a	81.959 Å
晶胞边长 b length_b	81.959 Å
晶胞边长 c length_c	222.978 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	48

空间群 space_group	P 65 2 2
空间群编号 int_tables_number	179
晶系 crystal_system	—

分辨率 resolution	2.600 Å
最低分辨率 resolution_low	29.060 Å
R 因子 r_factor	0.2440
R_work r_work	0.2440
R_free r_free	0.2630

描述 description	Phosphoribosyl-ATP pyrophosphatase
分子量 formula_weight	13678.2 kDa
EC 编号 ec_number	3.6.1.31
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	3157

Crystal structure of Phosphoribosyl-ATP pyrophosphohydrolase from Bacillus cereus. NESGC target BcR13.

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	Bacillus cereus
NCBI 分类编号 ncbi_taxonomy_id	1396
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	169

fit	/app/data/saxs_computation/yv/1yvw/1yvw.fit
pddf	/app/data/pr_computation/yv/1yvw/1yvw.pr.out
profile	/app/data/saxs_computation/yv/1yvw/1yvw.dat