2f4l

Crystal structure of a putative acetamidase (tm0119) from thermotoga maritima msb8 at 2.50 A resolution

Method: X-RAY DIFFRACTION D_max: 93.4 Å Quality: EXCELLENT

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

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2f4l
沉积日期 deposition_date	2005-11-23
结构标题 title	Crystal structure of a putative acetamidase (tm0119) from thermotoga maritima msb8 at 2.50 A resolution
关键词 keywords	Structural genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, hydrolase; HYDROLASE
实验方法 method	X-RAY DIFFRACTION

▼

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	32.21 Å
回转半径 Rg (电子) rg_electron	31.39 Å
零角强度 I(0) i0	218668000.00
分子量 molecular_weight	120550.0 kDa
排除体积 excluded_volume	151440 Å³
包络体积 envelope_volume	184190 Å³
水化壳体积 shell_volume	46900 Å³
包络直径 envelope_diameter	102.5 Å
壳层 Rg shell_rg	39.84 Å
包络 Rg envelope_rg	31.17 Å
形状 Rg shape_rg	31.39 Å
总 Rg total_rg	32.09 Å
总原子数 total_atoms	8365
残基数 n_residues	1072
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

▼

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	93.4 Å
Rg (实空间) rg_real	31.97 Å
Rg 误差 (实空间) rg_real_error	0.55 Å
I(0) (实空间) i0_real	2.1870e+08
I(0) 误差 (实空间) i0_real_error	3.0560e+06
Rg (倒空间) rg_reciprocal	32.07 Å
I(0) (倒空间) i0_reciprocal	218700000.0000
解质量估计 total_estimate	0.9064
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	43.8 Å
偏度 Skewness skewness	0.056
峰度 Kurtosis kurtosis	-0.567
角度范围 angular_range	— – 0.2450 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	114600000.0000
实空间数据点数 n_real_points	50
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.973; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.875

▶

4. 晶体学与实验 4. Crystallography & Experiment

▶

5. 实体与聚合体信息 (4)

Entity 1 polymer

描述 description	acetamidase, putative
分子量 formula_weight	33067.7 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	8546

MGSDKIHHHHHHMKVVPAQRCVYSFSANMAPVEEVYPGEQVVFETLDALGGSYDKIDFSKVNPATGPVFVNGVKPGDTLKVRIKRIELPRRGMIVTGKGFGVLGDEVEGFHTKELEIEKWAVLFDGVRIPIHPMVGVIGVAPQEGEYPTGTAHRHGGNMDTKEITENVTVHLPVFQEGALLALGDVHATMGDGEVCVSACEVPAKVVVEIDVSKEEIKWPVVETNDAYYIIVSLPDIEEALKEVTRETVWFIQRRKTIPFTDAYMLASLSVDVGISQLVNPAKTAKARIPKYIFTGV

来源 Source

来源生物 organism	Thermotoga maritima
NCBI 分类编号 ncbi_taxonomy_id	243274
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 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	2

Entity 4 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	163

▼

6. 折叠分类 (SCOP + CATH) 19 domains

SCOP 2.08 (7 domains)

结构域编号 domain_id	d2f4la1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.23 — CUB-like
超家族 Superfamily superfamily	b.23.3 — Acetamidase/Formamidase-like
家族 Family family	b.23.3.1 — Acetamidase/Formamidase-like

结构域编号 domain_id	d2f4lb2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.23 — CUB-like
超家族 Superfamily superfamily	b.23.3 — Acetamidase/Formamidase-like
家族 Family family	b.23.3.1 — Acetamidase/Formamidase-like

结构域编号 domain_id	d2f4lb3
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	d2f4lc2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.23 — CUB-like
超家族 Superfamily superfamily	b.23.3 — Acetamidase/Formamidase-like
家族 Family family	b.23.3.1 — Acetamidase/Formamidase-like

结构域编号 domain_id	d2f4lc3
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	d2f4ld2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.23 — CUB-like
超家族 Superfamily superfamily	b.23.3 — Acetamidase/Formamidase-like
家族 Family family	b.23.3.1 — Acetamidase/Formamidase-like

结构域编号 domain_id	d2f4ld3
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

CATH v4.4 (12 domains)

结构域编号 domain_id	2f4lA01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	580 — Acetamidase/Formamidase-like domains

结构域编号 domain_id	2f4lA02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	10 — Thrombin, subunit H
同源超家族 H-superfamily homologous superfamily	120 —

结构域编号 domain_id	2f4lA03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	28 — Endonuclease I-creI
同源超家族 H-superfamily homologous superfamily	20 — Acetamidase/Formamidase-like domains

结构域编号 domain_id	2f4lB01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	580 — Acetamidase/Formamidase-like domains

结构域编号 domain_id	2f4lB02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	10 — Thrombin, subunit H
同源超家族 H-superfamily homologous superfamily	120 —

结构域编号 domain_id	2f4lB03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	28 — Endonuclease I-creI
同源超家族 H-superfamily homologous superfamily	20 — Acetamidase/Formamidase-like domains

结构域编号 domain_id	2f4lC01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	580 — Acetamidase/Formamidase-like domains

结构域编号 domain_id	2f4lC02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	10 — Thrombin, subunit H
同源超家族 H-superfamily homologous superfamily	120 —

结构域编号 domain_id	2f4lC03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	28 — Endonuclease I-creI
同源超家族 H-superfamily homologous superfamily	20 — Acetamidase/Formamidase-like domains

结构域编号 domain_id	2f4lD01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	580 — Acetamidase/Formamidase-like domains

结构域编号 domain_id	2f4lD02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	10 — Thrombin, subunit H
同源超家族 H-superfamily homologous superfamily	120 —

结构域编号 domain_id	2f4lD03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	28 — Endonuclease I-creI
同源超家族 H-superfamily homologous superfamily	20 — Acetamidase/Formamidase-like domains

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	80.257 Å
晶胞边长 b length_b	104.068 Å
晶胞边长 c length_c	154.945 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	16

空间群 space_group	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	2.500 Å
最低分辨率 resolution_low	29.700 Å
R 因子 r_factor	—
R_work r_work	0.1920
R_free r_free	0.2420

fit	/app/data/saxs_computation/f4/2f4l/2f4l.fit
pddf	/app/data/pr_computation/f4/2f4l/2f4l.pr.out
profile	/app/data/saxs_computation/f4/2f4l/2f4l.dat