1w7v

ZnMg substituted aminopeptidase P from E. coli

Method: X-RAY DIFFRACTION D_max: 167.1 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	1w7v
沉积日期 deposition_date	2004-09-13
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; 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	607707000.00
分子量 molecular_weight	199670.0 kDa
排除体积 excluded_volume	248250 Å³
包络体积 envelope_volume	347410 Å³
水化壳体积 shell_volume	62455 Å³
包络直径 envelope_diameter	182.1 Å
壳层 Rg shell_rg	48.01 Å
包络 Rg envelope_rg	49.84 Å
形状 Rg shape_rg	50.03 Å
总 Rg total_rg	50.06 Å
总原子数 total_atoms	14042
残基数 n_residues	1761
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	2.17 Å
I(0) (实空间) i0_real	6.0770e+08
I(0) 误差 (实空间) i0_real_error	1.0550e+07
Rg (倒空间) rg_reciprocal	49.18 Å
I(0) (倒空间) i0_reciprocal	607100000.0000
解质量估计 total_estimate	0.7688
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	47.0 Å
偏度 Skewness skewness	0.636
峰度 Kurtosis kurtosis	-0.233
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	33350000.0000
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: 0.660; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.833; Smooth: 0.178

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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 (6)

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	15192

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 polymer

描述 description	PEPTIDE VAL-PRO-LEU
分子量 formula_weight	327.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	E,F,G,H

VPL

Entity 3 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 4 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 5 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 6 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	1094

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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	d1w7va1
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	d1w7va2
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	d1w7vb1
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	d1w7vb2
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	d1w7vc1
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	d1w7vc2
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	d1w7vd1
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	d1w7vd2
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	1w7vA01
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	1w7vA02
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	1w7vB01
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	1w7vB02
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	1w7vC01
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	1w7vC02
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	1w7vD01
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	1w7vD02
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	111.731 Å
晶胞边长 b length_b	236.527 Å
晶胞边长 c length_c	137.997 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	106.34 °
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	2.000 Å
最低分辨率 resolution_low	37.800 Å
R 因子 r_factor	0.1570
R_work r_work	0.1560
R_free r_free	0.1800

fit	/app/data/saxs_computation/w7/1w7v/1w7v.fit
pddf	/app/data/pr_computation/w7/1w7v/1w7v.pr.out
profile	/app/data/saxs_computation/w7/1w7v/1w7v.dat

ZnMg substituted aminopeptidase P from E. coli

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 (6)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 water

6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)