2btu

Crystal structure of Phosphoribosylformylglycinamidine cyclo-ligase from Bacillus Anthracis at 2.3A resolution.

Method: X-RAY DIFFRACTION D_max: 84.7 Å Quality: GOOD

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	2btu
沉积日期 deposition_date	2005-06-07
结构标题 title	Crystal structure of Phosphoribosylformylglycinamidine cyclo-ligase from Bacillus Anthracis at 2.3A resolution.
关键词 keywords	;SYNTHASE, PURM, DE NOVO PURINE BIOSYNTHESIS, AIR SYNTHASE FAMILY, SPINE, SYNTHETASE, FGAR AMIDOTRANSFERASE, NOVEL FOLD, STRUCTURAL PROTEOMICS IN EUROPE, STRUCTURAL GENOMICS ;; SYNTHASE
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	26.53 Å
回转半径 Rg (电子) rg_electron	25.84 Å
零角强度 I(0) i0	63545400.00
分子量 molecular_weight	62935.0 kDa
排除体积 excluded_volume	79068 Å³
包络体积 envelope_volume	98024 Å³
水化壳体积 shell_volume	31757 Å³
包络直径 envelope_diameter	87.7 Å
壳层 Rg shell_rg	33.52 Å
包络 Rg envelope_rg	25.89 Å
形状 Rg shape_rg	25.88 Å
总 Rg total_rg	26.58 Å
总原子数 total_atoms	4418
残基数 n_residues	629
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	84.7 Å
Rg (实空间) rg_real	26.52 Å
Rg 误差 (实空间) rg_real_error	0.54 Å
I(0) (实空间) i0_real	6.3550e+07
I(0) 误差 (实空间) i0_real_error	9.4830e+05
Rg (倒空间) rg_reciprocal	26.52 Å
I(0) (倒空间) i0_reciprocal	63550000.0000
解质量估计 total_estimate	0.8884
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	83.2 Å
偏度 Skewness skewness	0.398
峰度 Kurtosis kurtosis	-0.214
角度范围 angular_range	— – 0.3000 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	22050000.0000
实空间数据点数 n_real_points	61
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.869; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.937

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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	d2btua1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.79 — Bacillus chorismate mutase-like
超家族 Superfamily superfamily	d.79.4 — PurM N-terminal domain-like
家族 Family family	d.79.4.0 — automated matches

结构域编号 domain_id	d2btua2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.139 — PurM C-terminal domain-like
超家族 Superfamily superfamily	d.139.1 — PurM C-terminal domain-like
家族 Family family	d.139.1.0 — automated matches

结构域编号 domain_id	d2btub1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.79 — Bacillus chorismate mutase-like
超家族 Superfamily superfamily	d.79.4 — PurM N-terminal domain-like
家族 Family family	d.79.4.0 — automated matches

结构域编号 domain_id	d2btub2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.139 — PurM C-terminal domain-like
超家族 Superfamily superfamily	d.139.1 — PurM C-terminal domain-like
家族 Family family	d.139.1.0 — automated matches

CATH v4.4 (4 domains)

结构域编号 domain_id	2btuA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
同源超家族 H-superfamily homologous superfamily	10 — PurM-like, N-terminal domain

结构域编号 domain_id	2btuA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	650 — Phosphoribosyl-aminoimidazole Synthetase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — PurM-like C-terminal domain

结构域编号 domain_id	2btuB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
同源超家族 H-superfamily homologous superfamily	10 — PurM-like, N-terminal domain

结构域编号 domain_id	2btuB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	650 — Phosphoribosyl-aminoimidazole Synthetase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — PurM-like C-terminal domain

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7. 引用文献 (1)

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晶胞边长 a length_a	89.490 Å
晶胞边长 b length_b	89.490 Å
晶胞边长 c length_c	88.117 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	8

空间群 space_group	P 41
空间群编号 int_tables_number	76
晶系 crystal_system	—

分辨率 resolution	2.310 Å
最低分辨率 resolution_low	25.000 Å
R 因子 r_factor	—
R_work r_work	—
R_free r_free	0.2491

描述 description	PHOSPHORIBOSYL-AMINOIMIDAZOLE SYNTHETASE
分子量 formula_weight	37297.2 kDa
EC 编号 ec_number	6.3.3.1
来源方法 src_method	man
拷贝数 entity_count	2

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	4584

Crystal structure of Phosphoribosylformylglycinamidine cyclo-ligase from Bacillus Anthracis at 2.3A resolution.

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 ANTHRACIS
NCBI 分类编号 ncbi_taxonomy_id	1392
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	166

fit	/app/data/saxs_computation/bt/2btu/2btu.fit
pddf	/app/data/pr_computation/bt/2btu/2btu.pr.out
profile	/app/data/saxs_computation/bt/2btu/2btu.dat