1wbq

ZnMg substituted aminopeptidase P from E. coli

Method: X-RAY DIFFRACTION D_max: 167.1 Å Quality: REASONABLE

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	1wbq
沉积日期 deposition_date	2004-11-05
结构标题 title	ZnMg substituted aminopeptidase P from E. coli
关键词 keywords	HYDROLASE, PROLINE-SPECIFIC PEPTIDASE, METALLOENZYME, PITA-BREAD FOLD, DINUCLEAR HYDROLASE, METAL BINDING PROTEIN; 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	49.17 Å
回转半径 Rg (电子) rg_electron	50.06 Å
零角强度 I(0) i0	603542000.00
分子量 molecular_weight	198760.0 kDa
排除体积 excluded_volume	246990 Å³
包络体积 envelope_volume	346250 Å³
水化壳体积 shell_volume	62202 Å³
包络直径 envelope_diameter	182.0 Å
壳层 Rg shell_rg	48.13 Å
包络 Rg envelope_rg	49.91 Å
形状 Rg shape_rg	50.04 Å
总 Rg total_rg	50.07 Å
总原子数 total_atoms	13978
残基数 n_residues	1753
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	167.1 Å
Rg (实空间) rg_real	50.00 Å
Rg 误差 (实空间) rg_real_error	1.99 Å
I(0) (实空间) i0_real	6.0350e+08
I(0) 误差 (实空间) i0_real_error	1.2200e+07
Rg (倒空间) rg_reciprocal	49.18 Å
I(0) (倒空间) i0_reciprocal	602900000.0000
解质量估计 total_estimate	0.5574
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	47.0 Å
偏度 Skewness skewness	0.636
峰度 Kurtosis kurtosis	-0.234
角度范围 angular_range	— – 0.1600 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	33180000.0000
实空间数据点数 n_real_points	33
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.658; Stabil: 1.000; Sysdev: 0.087; Positv: 1.000; Valcen: 0.832; Smooth: 0.176

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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 (5)

Entity 1 polymer

描述 description	XAA-PRO AMINOPEPTIDASE
分子量 formula_weight	49792.1 kDa
EC 编号 ec_number	3.4.11.9
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	14814

SEISRQEFQRRRQALVEQMQPGSAALIFAAPEVTRSADSEYPYRQNSDFWYFTGFNEPEAVLVLIKSDDTHNHSVLFNRVRDLTAEIWFGRRLGQDAAPEKLGVDRALAFSEINQQLYQLLNGLDVVYHAQGEYAYADVIVNSALEKLRKGSRQNLTAPATMIDWRPVVHEMRLFKSPEEIAVLRRAGEITAMAHTRAMEKCRPGMFEYHLEGEIHHEFNRHGARYPSYNTIVGSGENGCILHYTENECEMRDGDLVLIDAGCEYKGYAGDITRTFPVNGKFTQAQREIYDIVLESLETSLRLYRPGTSILEVTGEVVRIMVSGLVKLGILKGDVDELIAQNAHRPFFMHGLSHWLGLDVHDVGVYGQDRSRILEPGMVLTVEPGLYIAPDAEVPEQYRGIGIRIEDDIVITETGNENLTASVVKKPEEIEALMVAARKQ

来源 Source

来源生物 organism	ESCHERICHIA COLI
NCBI 分类编号 ncbi_taxonomy_id	562
宿主生物 host_organism	ESCHERICHIA COLI

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 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

Entity 4 non-polymer

描述 description	CHLORIDE ION
分子量 formula_weight	35.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 5 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	832

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6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d1wbqa1
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	d1wbqa2
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	d1wbqb1
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	d1wbqb2
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	d1wbqc1
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	d1wbqc2
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	d1wbqd1
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	d1wbqd2
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 (8 domains)

结构域编号 domain_id	1wbqA01
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	1wbqA02
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	1wbqB01
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	1wbqB02
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	1wbqC01
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	1wbqC02
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	1wbqD01
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	1wbqD02
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 (1)

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晶胞边长 a length_a	111.974 Å
晶胞边长 b length_b	236.703 Å
晶胞边长 c length_c	137.637 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	106.14 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	16

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	—

分辨率 resolution	2.300 Å
最低分辨率 resolution_low	29.970 Å
R 因子 r_factor	0.1680
R_work r_work	0.1670
R_free r_free	0.1970

fit	/app/data/saxs_computation/wb/1wbq/1wbq.fit
pddf	/app/data/pr_computation/wb/1wbq/1wbq.pr.out
profile	/app/data/saxs_computation/wb/1wbq/1wbq.dat