SAXSdb — 1pv9

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1pv9
沉积日期 deposition_date	2003-06-27
结构标题 title	Prolidase from Pyrococcus furiosus
关键词 keywords	prolidase, peptidase, 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	26.69 Å
回转半径 Rg (电子) rg_electron	25.52 Å
零角强度 I(0) i0	84924100.00
分子量 molecular_weight	74081.0 kDa
排除体积 excluded_volume	93609 Å³
包络体积 envelope_volume	115850 Å³
水化壳体积 shell_volume	36509 Å³
包络直径 envelope_diameter	84.8 Å
壳层 Rg shell_rg	34.09 Å
包络 Rg envelope_rg	25.28 Å
形状 Rg shape_rg	25.52 Å
总 Rg total_rg	26.45 Å
总原子数 total_atoms	5200
残基数 n_residues	655
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	80.7 Å
Rg (实空间) rg_real	26.49 Å
Rg 误差 (实空间) rg_real_error	0.50 Å
I(0) (实空间) i0_real	8.4920e+07
I(0) 误差 (实空间) i0_real_error	1.1150e+06
Rg (倒空间) rg_reciprocal	26.55 Å
I(0) (倒空间) i0_reciprocal	84930000.0000
解质量估计 total_estimate	0.8997
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	36.9 Å
偏度 Skewness skewness	0.062
峰度 Kurtosis kurtosis	-0.478
角度范围 angular_range	— – 0.2950 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	25880000.0000
实空间数据点数 n_real_points	60
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.917; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.965

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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 (3)

Entity 1 polymer

描述 description	Xaa-Pro dipeptidase
分子量 formula_weight	39443.2 kDa
EC 编号 ec_number	3.4.13.9
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	5376

MKERLEKLVKFMDENSIDRVFIAKPVNVYYFSGTSPLGGGYIIVDGDEATLYVPELEYEMAKEESKLPVVKFKKFDEIYEILKNTETLGIEGTLSYSMVENFKEKSNVKEFKKIDDVIKDLRIIKTKEEIEIIEKACEIADKAVMAAIEEITEGKREREVAAKVEYLMKMNGAEKPAFDTIIASGHRSALPHGVASDKRIERGDLVVIDLGALYNHYNSDITRTIVVGSPNEKQREIYEIVLEAQKRAVEAAKPGMTAKELDSIAREIIKEYGYGDYFIHSLGHGVGLEIHEWPRISQYDETVLKEGMVITIEPGIYIPKLGGVRIEDTVLITENGAKRLTKTERELL

来源 Source

来源生物 organism	Pyrococcus furiosus
NCBI 分类编号 ncbi_taxonomy_id	2261
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

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	176

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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	d1pv9a1
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.55.2 — Creatinase/prolidase N-terminal domain
家族 Family family	c.55.2.1 — Creatinase/prolidase N-terminal domain

结构域编号 domain_id	d1pv9a2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.127 — Creatinase/aminopeptidase
超家族 Superfamily superfamily	d.127.1 — Creatinase/aminopeptidase
家族 Family family	d.127.1.1 — Creatinase/aminopeptidase

结构域编号 domain_id	d1pv9b1
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.55.2 — Creatinase/prolidase N-terminal domain
家族 Family family	c.55.2.1 — Creatinase/prolidase N-terminal domain

结构域编号 domain_id	d1pv9b2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.127 — Creatinase/aminopeptidase
超家族 Superfamily superfamily	d.127.1 — Creatinase/aminopeptidase
家族 Family family	d.127.1.1 — Creatinase/aminopeptidase

CATH v4.4 (4 domains)

结构域编号 domain_id	1pv9A01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	350 — Creatine Amidinohydrolase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Creatinase/prolidase N-terminal domain

结构域编号 domain_id	1pv9A02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	230 — Creatine Amidinohydrolase
同源超家族 H-superfamily homologous superfamily	10 — Creatinase/methionine aminopeptidase superfamily

结构域编号 domain_id	1pv9B01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	350 — Creatine Amidinohydrolase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Creatinase/prolidase N-terminal domain

结构域编号 domain_id	1pv9B02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	230 — Creatine Amidinohydrolase
同源超家族 H-superfamily homologous superfamily	10 — Creatinase/methionine aminopeptidase superfamily

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7. 引用文献 (3)

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晶胞边长 a length_a	56.476 Å
晶胞边长 b length_b	97.227 Å
晶胞边长 c length_c	69.882 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	97.09 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

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	2.000 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.2464
R_work r_work	0.2447
R_free r_free	0.2773

fit	/app/data/saxs_computation/pv/1pv9/1pv9.fit
pddf	/app/data/pr_computation/pv/1pv9/1pv9.pr.out
profile	/app/data/saxs_computation/pv/1pv9/1pv9.dat

Prolidase from Pyrococcus furiosus

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