1z7a

Crystal structure of probable Polysaccharide deacetylase from Pseudomonas aeruginosa PAO1

Method: X-RAY DIFFRACTION D_max: 164.6 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	1z7a
沉积日期 deposition_date	2005-03-24
结构标题 title	Crystal structure of probable Polysaccharide deacetylase from Pseudomonas aeruginosa PAO1
关键词 keywords	;Hypothetical protein structural genomics, PSI, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG, UNKNOWN FUNCTION ;; UNKNOWN FUNCTION
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	48.64 Å
回转半径 Rg (电子) rg_electron	48.86 Å
零角强度 I(0) i0	1271640000.00
分子量 molecular_weight	284900.0 kDa
排除体积 excluded_volume	349440 Å³
包络体积 envelope_volume	422400 Å³
水化壳体积 shell_volume	73326 Å³
包络直径 envelope_diameter	170.4 Å
壳层 Rg shell_rg	50.60 Å
包络 Rg envelope_rg	48.63 Å
形状 Rg shape_rg	48.84 Å
总 Rg total_rg	48.96 Å
总原子数 total_atoms	19804
残基数 n_residues	2318
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	164.6 Å
Rg (实空间) rg_real	49.06 Å
Rg 误差 (实空间) rg_real_error	1.55 Å
I(0) (实空间) i0_real	1.2720e+09
I(0) 误差 (实空间) i0_real_error	2.4130e+07
Rg (倒空间) rg_reciprocal	48.64 Å
I(0) (倒空间) i0_reciprocal	1271000000.0000
解质量估计 total_estimate	0.8208
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	46.3 Å
偏度 Skewness skewness	0.476
峰度 Kurtosis kurtosis	-0.504
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	113400000.0000
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: 0.769; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.899; Smooth: 0.461

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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	conserved hypothetical protein
分子量 formula_weight	36272.9 kDa
来源方法 src_method	man
拷贝数 entity_count	8

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F,G,H
原子数 atom_count	22756

MSADYPRDLIGYGNNPPHPHWPGDARIALSFVLNYEEGGERCVLHGDKESEAFLSEMVAAQPLQGVRHMSMESLYEYGSRAGVWRLLKLFKRRNVPLTVFAVAMAAQRNPEVIRAMVADGHEICSHGYRWIDYQYMDEAQEREHMLEAIRILTELTGQRPVGWYTGRTGPNTRRLVMEEGGFLYDSDTYDDDLPYWDPASTAEKPHLVIPYTLDTNDMRFTQVQGFNNGEQFFQYLKDAFDVLYEEGATAPKMLSIGLHCRLIGRPARMAALERFIQYAQSHDKVWFARREDIARHWHREHPFQETEA

来源 Source

来源生物 organism	Pseudomonas aeruginosa
NCBI 分类编号 ncbi_taxonomy_id	208964
宿主生物 host_organism	Escherichia coli BL21

Entity 2 non-polymer

描述 description	1,2-ETHANEDIOL
分子量 formula_weight	62.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	19

Entity 3 non-polymer

描述 description	GLYCEROL
分子量 formula_weight	92.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	7

Entity 4 non-polymer

描述 description	ISOPROPYL ALCOHOL
分子量 formula_weight	60.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	8

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	2141

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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	d1z7aa1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.6 — 7-stranded beta/alpha barrel
超家族 Superfamily superfamily	c.6.2 — Glycoside hydrolase/deacetylase
家族 Family family	c.6.2.6 — PA1517-like

结构域编号 domain_id	d1z7ab_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.6 — 7-stranded beta/alpha barrel
超家族 Superfamily superfamily	c.6.2 — Glycoside hydrolase/deacetylase
家族 Family family	c.6.2.6 — PA1517-like

结构域编号 domain_id	d1z7ac_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.6 — 7-stranded beta/alpha barrel
超家族 Superfamily superfamily	c.6.2 — Glycoside hydrolase/deacetylase
家族 Family family	c.6.2.6 — PA1517-like

结构域编号 domain_id	d1z7ad_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.6 — 7-stranded beta/alpha barrel
超家族 Superfamily superfamily	c.6.2 — Glycoside hydrolase/deacetylase
家族 Family family	c.6.2.6 — PA1517-like

结构域编号 domain_id	d1z7ae_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.6 — 7-stranded beta/alpha barrel
超家族 Superfamily superfamily	c.6.2 — Glycoside hydrolase/deacetylase
家族 Family family	c.6.2.6 — PA1517-like

结构域编号 domain_id	d1z7af_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.6 — 7-stranded beta/alpha barrel
超家族 Superfamily superfamily	c.6.2 — Glycoside hydrolase/deacetylase
家族 Family family	c.6.2.6 — PA1517-like

结构域编号 domain_id	d1z7ag_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.6 — 7-stranded beta/alpha barrel
超家族 Superfamily superfamily	c.6.2 — Glycoside hydrolase/deacetylase
家族 Family family	c.6.2.6 — PA1517-like

结构域编号 domain_id	d1z7ah_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.6 — 7-stranded beta/alpha barrel
超家族 Superfamily superfamily	c.6.2 — Glycoside hydrolase/deacetylase
家族 Family family	c.6.2.6 — PA1517-like

CATH v4.4 (8 domains)

结构域编号 domain_id	1z7aA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	370 — Glycoside hydrolase/deacetylase

结构域编号 domain_id	1z7aB00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	370 — Glycoside hydrolase/deacetylase

结构域编号 domain_id	1z7aC00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	370 — Glycoside hydrolase/deacetylase

结构域编号 domain_id	1z7aD00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	370 — Glycoside hydrolase/deacetylase

结构域编号 domain_id	1z7aE00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	370 — Glycoside hydrolase/deacetylase

结构域编号 domain_id	1z7aF00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	370 — Glycoside hydrolase/deacetylase

结构域编号 domain_id	1z7aG00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	370 — Glycoside hydrolase/deacetylase

结构域编号 domain_id	1z7aH00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	370 — Glycoside hydrolase/deacetylase

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7. 引用文献 (1)

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晶胞边长 a length_a	101.653 Å
晶胞边长 b length_b	101.773 Å
晶胞边长 c length_c	100.990 Å
晶胞夹角 α angle_alpha	60.71 °
晶胞夹角 β angle_beta	61.24 °
晶胞夹角 γ angle_gamma	89.90 °
晶胞分子数 Z z_pdb	8

空间群 space_group	P 1
空间群编号 int_tables_number	1
晶系 crystal_system	—

分辨率 resolution	1.710 Å
最低分辨率 resolution_low	50.000 Å
R 因子 r_factor	0.1522
R_work r_work	0.1510
R_free r_free	0.1746

fit	/app/data/saxs_computation/z7/1z7a/1z7a.fit
pddf	/app/data/pr_computation/z7/1z7a/1z7a.pr.out
profile	/app/data/saxs_computation/z7/1z7a/1z7a.dat