1iof

;X-RAY CRYSTALLINE STRUCTURES OF PYRROLIDONE CARBOXYL PEPTIDASE FROM A HYPERTHERMOPHILE, PYROCOCCUS FURIOSUS, AND ITS CYS-FREE MUTANT ;

Method: X-RAY DIFFRACTION D_max: 93.2 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

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1iof
沉积日期 deposition_date	2001-03-09
结构标题 title	;X-RAY CRYSTALLINE STRUCTURES OF PYRROLIDONE CARBOXYL PEPTIDASE FROM A HYPERTHERMOPHILE, PYROCOCCUS FURIOSUS, AND ITS CYS-FREE MUTANT ;
关键词 keywords	PGP-I, PYROGLUTAMYL-PEPTIDASE I, PCP, protease, Pyrococcus furiosus, Archaea, 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	29.84 Å
回转半径 Rg (电子) rg_electron	29.10 Å
零角强度 I(0) i0	116834000.00
分子量 molecular_weight	91279.0 kDa
排除体积 excluded_volume	116860 Å³
包络体积 envelope_volume	139020 Å³
水化壳体积 shell_volume	39549 Å³
包络直径 envelope_diameter	92.0 Å
壳层 Rg shell_rg	36.90 Å
包络 Rg envelope_rg	28.53 Å
形状 Rg shape_rg	29.09 Å
总 Rg total_rg	29.90 Å
总原子数 total_atoms	6420
残基数 n_residues	832
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	93.2 Å
Rg (实空间) rg_real	29.71 Å
Rg 误差 (实空间) rg_real_error	0.54 Å
I(0) (实空间) i0_real	1.1680e+08
I(0) 误差 (实空间) i0_real_error	1.7380e+06
Rg (倒空间) rg_reciprocal	29.76 Å
I(0) (倒空间) i0_reciprocal	116800000.0000
解质量估计 total_estimate	0.9064
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	37.0 Å
偏度 Skewness skewness	0.165
峰度 Kurtosis kurtosis	-0.550
角度范围 angular_range	— – 0.2650 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	37450000.0000
实空间数据点数 n_real_points	54
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.941; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.958

▶

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	d1iofa_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.56 — Phosphorylase/hydrolase-like
超家族 Superfamily superfamily	c.56.4 — Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase)
家族 Family family	c.56.4.1 — Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase)

结构域编号 domain_id	d1iofb_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.56 — Phosphorylase/hydrolase-like
超家族 Superfamily superfamily	c.56.4 — Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase)
家族 Family family	c.56.4.1 — Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase)

结构域编号 domain_id	d1iofc_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.56 — Phosphorylase/hydrolase-like
超家族 Superfamily superfamily	c.56.4 — Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase)
家族 Family family	c.56.4.1 — Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase)

结构域编号 domain_id	d1iofd_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.56 — Phosphorylase/hydrolase-like
超家族 Superfamily superfamily	c.56.4 — Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase)
家族 Family family	c.56.4.1 — Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase)

CATH v4.4 (4 domains)

结构域编号 domain_id	1iofA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	630 — Aminopeptidase
同源超家族 H-superfamily homologous superfamily	20 — Peptidase C15, pyroglutamyl peptidase I-like

结构域编号 domain_id	1iofB00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	630 — Aminopeptidase
同源超家族 H-superfamily homologous superfamily	20 — Peptidase C15, pyroglutamyl peptidase I-like

结构域编号 domain_id	1iofC00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	630 — Aminopeptidase
同源超家族 H-superfamily homologous superfamily	20 — Peptidase C15, pyroglutamyl peptidase I-like

结构域编号 domain_id	1iofD00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	630 — Aminopeptidase
同源超家族 H-superfamily homologous superfamily	20 — Peptidase C15, pyroglutamyl peptidase I-like

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	57.900 Å
晶胞边长 b length_b	105.000 Å
晶胞边长 c length_c	78.500 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.70 °
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	2.200 Å
最低分辨率 resolution_low	10.000 Å
R 因子 r_factor	—
R_work r_work	0.1950
R_free r_free	0.2320

描述 description	PYRROLIDONE CARBOXYL PEPTIDASE
分子量 formula_weight	22851.8 kDa
EC 编号 ec_number	3.4.19.3
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	6588

;X-RAY CRYSTALLINE STRUCTURES OF PYRROLIDONE CARBOXYL PEPTIDASE FROM A HYPERTHERMOPHILE, PYROCOCCUS FURIOSUS, AND ITS CYS-FREE MUTANT ;

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	Pyrococcus furiosus
NCBI 分类编号 ncbi_taxonomy_id	2261
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	168

fit	/app/data/saxs_computation/io/1iof/1iof.fit
pddf	/app/data/pr_computation/io/1iof/1iof.pr.out
profile	/app/data/saxs_computation/io/1iof/1iof.dat