1xfo

Crystal Structure of an archaeal aminopeptidase

Method: X-RAY DIFFRACTION D_max: 118.2 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	1xfo
沉积日期 deposition_date	2004-09-15
结构标题 title	Crystal Structure of an archaeal aminopeptidase
关键词 keywords	aminopeptidase, self-compartmentalizing, metalloprotease, 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	36.46 Å
回转半径 Rg (电子) rg_electron	36.04 Å
零角强度 I(0) i0	319809000.00
分子量 molecular_weight	149650.0 kDa
排除体积 excluded_volume	189400 Å³
包络体积 envelope_volume	238030 Å³
水化壳体积 shell_volume	54336 Å³
包络直径 envelope_diameter	129.9 Å
壳层 Rg shell_rg	43.04 Å
包络 Rg envelope_rg	35.85 Å
形状 Rg shape_rg	36.05 Å
总 Rg total_rg	36.48 Å
总原子数 total_atoms	10522
残基数 n_residues	1357
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	118.2 Å
Rg (实空间) rg_real	36.46 Å
Rg 误差 (实空间) rg_real_error	0.99 Å
I(0) (实空间) i0_real	3.1980e+08
I(0) 误差 (实空间) i0_real_error	5.0940e+06
Rg (倒空间) rg_reciprocal	36.46 Å
I(0) (倒空间) i0_reciprocal	319800000.0000
解质量估计 total_estimate	0.8830
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	44.0 Å
偏度 Skewness skewness	0.348
峰度 Kurtosis kurtosis	-0.306
角度范围 angular_range	— – 0.2150 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	136300000.0000
实空间数据点数 n_real_points	44
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.907; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.764

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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	Frv operon protein FrvX
分子量 formula_weight	39510.5 kDa
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	11167

RGSHMEVRNMVDYELLKKVVEAPGVSGYEFLGIRDVVIEEIKDYVDEVKVDKLGNVIAHKKGEGPKVMIAAHMDQIGLMVTHIEKNGFLRVAPIGGVDPKTLIAQRFKVWIDKGKFIYGVGASVPPHIQKPEDRKKAPDWDQIFIDIGAESKEEAEDMGVKIGTVITWDGRLERLGKHRFVSIAFDDRIAVYTILEVAKQLKDAKADVYFVATVQEEVGLRGARTSAFGIEPDYGFAIDVTIAADIPGTPEHKQVTHLGKGTAIKIMDRSVICHPTIVRWLEELAKKHEIPYQLEILLGGGTDAGAIHLTKAGVPTGALSVPARYIHSNTEVVDERDVDATVELMTKALENIHELKI

来源 Source

来源生物 organism	Pyrococcus horikoshii
NCBI 分类编号 ncbi_taxonomy_id	53953
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	8

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	645

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6. 折叠分类 (SCOP + CATH) 17 domains

SCOP 2.08 (9 domains)

结构域编号 domain_id	d1xfoa1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.49 — Domain of alpha and beta subunits of F1 ATP synthase-like
超家族 Superfamily superfamily	b.49.3 — Aminopeptidase/glucanase lid domain
家族 Family family	b.49.3.1 — Aminopeptidase/glucanase lid domain

结构域编号 domain_id	d1xfoa2
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.56.5 — Zn-dependent exopeptidases
家族 Family family	c.56.5.4 — Bacterial dinuclear zinc exopeptidases

结构域编号 domain_id	d1xfoa3
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d1xfob1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.49 — Domain of alpha and beta subunits of F1 ATP synthase-like
超家族 Superfamily superfamily	b.49.3 — Aminopeptidase/glucanase lid domain
家族 Family family	b.49.3.1 — Aminopeptidase/glucanase lid domain

结构域编号 domain_id	d1xfob2
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.56.5 — Zn-dependent exopeptidases
家族 Family family	c.56.5.4 — Bacterial dinuclear zinc exopeptidases

结构域编号 domain_id	d1xfoc1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.49 — Domain of alpha and beta subunits of F1 ATP synthase-like
超家族 Superfamily superfamily	b.49.3 — Aminopeptidase/glucanase lid domain
家族 Family family	b.49.3.1 — Aminopeptidase/glucanase lid domain

结构域编号 domain_id	d1xfoc2
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.56.5 — Zn-dependent exopeptidases
家族 Family family	c.56.5.4 — Bacterial dinuclear zinc exopeptidases

结构域编号 domain_id	d1xfod1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.49 — Domain of alpha and beta subunits of F1 ATP synthase-like
超家族 Superfamily superfamily	b.49.3 — Aminopeptidase/glucanase lid domain
家族 Family family	b.49.3.1 — Aminopeptidase/glucanase lid domain

结构域编号 domain_id	d1xfod2
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.56.5 — Zn-dependent exopeptidases
家族 Family family	c.56.5.4 — Bacterial dinuclear zinc exopeptidases

CATH v4.4 (8 domains)

结构域编号 domain_id	1xfoA01
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	10 — Zn peptidases

结构域编号 domain_id	1xfoA02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
同源超家族 H-superfamily homologous superfamily	40 — Peptidase M42, domain 2

结构域编号 domain_id	1xfoB01
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	10 — Zn peptidases

结构域编号 domain_id	1xfoB02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
同源超家族 H-superfamily homologous superfamily	40 — Peptidase M42, domain 2

结构域编号 domain_id	1xfoC01
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	10 — Zn peptidases

结构域编号 domain_id	1xfoC02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
同源超家族 H-superfamily homologous superfamily	40 — Peptidase M42, domain 2

结构域编号 domain_id	1xfoD01
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	10 — Zn peptidases

结构域编号 domain_id	1xfoD02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
同源超家族 H-superfamily homologous superfamily	40 — Peptidase M42, domain 2

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7. 引用文献 (1)

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晶胞边长 a length_a	158.340 Å
晶胞边长 b length_b	158.340 Å
晶胞边长 c length_c	114.460 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	120.00 °
晶胞分子数 Z z_pdb	24

空间群 space_group	P 63
空间群编号 int_tables_number	173
晶系 crystal_system	—

分辨率 resolution	1.960 Å
最低分辨率 resolution_low	29.920 Å
R 因子 r_factor	0.1834
R_work r_work	0.1828
R_free r_free	0.2093

fit	/app/data/saxs_computation/xf/1xfo/1xfo.fit
pddf	/app/data/pr_computation/xf/1xfo/1xfo.pr.out
profile	/app/data/saxs_computation/xf/1xfo/1xfo.dat