1m35

Aminopeptidase P from Escherichia coli

Method: X-RAY DIFFRACTION D_max: 192.0 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	1m35
沉积日期 deposition_date	2002-06-27
结构标题 title	Aminopeptidase P from Escherichia coli
关键词 keywords	Aminopeptidase, proline specific, manganese enzyme, 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	59.07 Å
回转半径 Rg (电子) rg_electron	59.80 Å
零角强度 I(0) i0	1325580000.00
分子量 molecular_weight	298650.0 kDa
排除体积 excluded_volume	371300 Å³
包络体积 envelope_volume	555830 Å³
水化壳体积 shell_volume	82761 Å³
包络直径 envelope_diameter	213.2 Å
壳层 Rg shell_rg	55.26 Å
包络 Rg envelope_rg	58.97 Å
形状 Rg shape_rg	59.76 Å
总 Rg total_rg	59.82 Å
总原子数 total_atoms	21006
残基数 n_residues	2640
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	192.0 Å
Rg (实空间) rg_real	59.68 Å
Rg 误差 (实空间) rg_real_error	2.02 Å
I(0) (实空间) i0_real	1.3260e+09
I(0) 误差 (实空间) i0_real_error	3.1360e+07
Rg (倒空间) rg_reciprocal	58.50 Å
I(0) (倒空间) i0_reciprocal	1323000000.0000
解质量估计 total_estimate	0.7994
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	49.8 Å
偏度 Skewness skewness	0.508
峰度 Kurtosis kurtosis	-0.497
角度范围 angular_range	— – 0.1350 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	68390000.0000
实空间数据点数 n_real_points	28
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.823; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.850; Smooth: 0.069

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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	AMINOPEPTIDASE P
分子量 formula_weight	49744.1 kDa
EC 编号 ec_number	3.4.11.9
来源方法 src_method	man
拷贝数 entity_count	6

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F
原子数 atom_count	22624

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	MANGANESE (II) ION
分子量 formula_weight	54.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	12

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	1618

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6. 折叠分类 (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

结构域编号 domain_id	d1m35a1
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	d1m35a2
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	d1m35b1
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	d1m35b2
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	d1m35c1
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	d1m35c2
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	d1m35d1
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	d1m35d2
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	d1m35e1
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	d1m35e2
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	d1m35f1
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	d1m35f2
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 (12 domains)

结构域编号 domain_id	1m35A01
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	1m35A02
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	1m35B01
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	1m35B02
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	1m35C01
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	1m35C02
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	1m35D01
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	1m35D02
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	1m35E01
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	1m35E02
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	1m35F01
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	1m35F02
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 (2)

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晶胞边长 a length_a	209.047 Å
晶胞边长 b length_b	313.963 Å
晶胞边长 c length_c	162.034 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	48

空间群 space_group	C 2 2 21
空间群编号 int_tables_number	20
晶系 crystal_system	—

分辨率 resolution	2.400 Å
最低分辨率 resolution_low	19.990 Å
R 因子 r_factor	—
R_work r_work	0.1950
R_free r_free	0.2150

fit	/app/data/saxs_computation/m3/1m35/1m35.fit
pddf	/app/data/pr_computation/m3/1m35/1m35.pr.out
profile	/app/data/saxs_computation/m3/1m35/1m35.dat