8gtu

;Crystal Structure of putative amino acid binding periplasmic ABC transporter protein from Candidatus Liberibacter asiaticus in complex with Clidinium ;

Method: X-RAY DIFFRACTION D_max: 78.3 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

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8gtu
沉积日期 deposition_date	2022-09-08
结构标题 title	;Crystal Structure of putative amino acid binding periplasmic ABC transporter protein from Candidatus Liberibacter asiaticus in complex with Clidinium ;
关键词 keywords	amino acid binding receptors, periplasmic amino acid binding protein, Candidatus Liberibacter asiaticus, TRANSPORT PROTEIN; TRANSPORT PROTEIN
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	25.50 Å
回转半径 Rg (电子) rg_electron	24.26 Å
零角强度 I(0) i0	46844600.00
分子量 molecular_weight	54150.0 kDa
排除体积 excluded_volume	68307 Å³
包络体积 envelope_volume	81267 Å³
水化壳体积 shell_volume	28027 Å³
包络直径 envelope_diameter	81.1 Å
壳层 Rg shell_rg	31.63 Å
包络 Rg envelope_rg	24.36 Å
形状 Rg shape_rg	24.26 Å
总 Rg total_rg	25.14 Å
总原子数 total_atoms	3822
残基数 n_residues	470
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	78.3 Å
Rg (实空间) rg_real	25.45 Å
Rg 误差 (实空间) rg_real_error	0.50 Å
I(0) (实空间) i0_real	4.6840e+07
I(0) 误差 (实空间) i0_real_error	6.6540e+05
Rg (倒空间) rg_reciprocal	25.47 Å
I(0) (倒空间) i0_reciprocal	46850000.0000
解质量估计 total_estimate	0.9095
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	27.8 Å
偏度 Skewness skewness	0.274
峰度 Kurtosis kurtosis	-0.525
角度范围 angular_range	— – 0.3100 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	10850000.0000
实空间数据点数 n_real_points	63
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.948; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.975

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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	Putative amino acid-binding periplasmic ABC transporter protein
分子量 formula_weight	27615.6 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	4105

MFRTEDQSALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLNLKVEFFETAVSGLITGLDTNRYDVLVNVAITPERQKKYDFSIPYIAHRVLLVVRSDQQDIRSFKDLTDKTVAQILGTDLSRFAKELKSHLVFSHNFEQSLQLLLSKRTDATMIPDIPFFNFLERRPHDGNLFKIADRMKDNSAVAFMMRKGNNKLTRSINEILCAIHLDGTYKKIFDRYFDKNIISSVPGCSS

来源 Source

来源生物 organism	Liberibacter asiaticus (strain psy62)
NCBI 分类编号 ncbi_taxonomy_id	537021
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	[(3~{S})-1-methyl-1-azoniabicyclo[2.2.2]octan-3-yl] 2-oxidanyl-2,2-diphenyl-ethanoate
分子量 formula_weight	352.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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	97

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7. 引用文献 (1)

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晶胞边长 a length_a	45.600 Å
晶胞边长 b length_b	87.440 Å
晶胞边长 c length_c	123.310 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	8

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	2.560 Å
最低分辨率 resolution_low	50.440 Å
R 因子 r_factor	0.2151
R_work r_work	0.2113
R_free r_free	0.2915

fit	/app/data/saxs_computation/gt/8gtu/8gtu.fit
pddf	/app/data/pr_computation/gt/8gtu/8gtu.pr.out
profile	/app/data/saxs_computation/gt/8gtu/8gtu.dat

;Crystal Structure of putative amino acid binding periplasmic ABC transporter protein from Candidatus Liberibacter asiaticus in complex with Clidinium ;

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