8iq9

Crystal structure of trimeric K2-2 TSP in complex with tetrasaccharide and octasaccharide

Method: X-RAY DIFFRACTION D_max: 120.1 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	8iq9
沉积日期 deposition_date	2023-03-16
结构标题 title	Crystal structure of trimeric K2-2 TSP in complex with tetrasaccharide and octasaccharide
关键词 keywords	bacteriophage, tailspike protein, Klebsiella pneumoniae K2, 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	36.36 Å
回转半径 Rg (电子) rg_electron	35.87 Å
零角强度 I(0) i0	524171000.00
分子量 molecular_weight	184300.0 kDa
排除体积 excluded_volume	229310 Å³
包络体积 envelope_volume	266580 Å³
水化壳体积 shell_volume	60471 Å³
包络直径 envelope_diameter	129.8 Å
壳层 Rg shell_rg	43.17 Å
包络 Rg envelope_rg	36.55 Å
形状 Rg shape_rg	35.86 Å
总 Rg total_rg	36.29 Å
总原子数 total_atoms	12954
残基数 n_residues	1693
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	120.1 Å
Rg (实空间) rg_real	36.39 Å
Rg 误差 (实空间) rg_real_error	0.71 Å
I(0) (实空间) i0_real	5.2420e+08
I(0) 误差 (实空间) i0_real_error	8.4210e+06
Rg (倒空间) rg_reciprocal	36.37 Å
I(0) (倒空间) i0_reciprocal	524200000.0000
解质量估计 total_estimate	0.8615
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	43.7 Å
偏度 Skewness skewness	0.464
峰度 Kurtosis kurtosis	-0.051
角度范围 angular_range	— – 0.2200 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	165700000.0000
实空间数据点数 n_real_points	45
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.788; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.831

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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 (6)

Entity 1 polymer

描述 description	K2-2 TSP
分子量 formula_weight	64814.4 kDa
来源方法 src_method	man
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C
原子数 atom_count	15282

MGHHHHHHHHHHSSGHGTIQGSEDLYFQSHMMALVDLVRAGGYSVEYPQFSSMAKLKAFPHSEDGQLVRLLSWHEGVGLGGGLFKVSTSSTATGNDGTVVVASNGVRLLRVVNGPIWADMFGALPNSDIDSMPAVAAAYAYAASVNTDLYIGVATYKFKGSTPINVDPSRAGIIGYQGKVRIDCSEFTGSIVFSINSSYSYTPAAYYNNLSPALQGLYVFGAKTSGVDGLLVGRETVGSDKSYNGQTEVRECTFDKFDRNIRMGHNSWRFVFYKVNSLNALSPNGILYVPAGLDDSGEILSFYHCQFFDGAGSNIRLSCSSYTMVFNTCSFLNITFFVDSASSATVTCNGCNFANPGSASTRRYVDISAGHTNVFNIIGGSIVTNSNPGQTQALLYVSTDNLLNLVGVTAPYGGHYQQEQELGYHAFIGGAGTVTTSGVMLQLRNGAGTCPLHSSLSTFSNWNFGYGNLNAWTVDKGTGTSSVVEYLANAGPKGTEGAMRVAPVSVGTNVSQVQAVTNPGMFSMSCMVNIATTPGNAGQVSIGFLDAAGNSLPGGVSANLGTTTGWQVIGKNTLRGKVPIGAKQVRVNIQTVAGADVKYAYLLCNVVKKLGC

来源 Source

来源生物 organism	Klebsiella phage VLC6
NCBI 分类编号 ncbi_taxonomy_id	2723743
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 branched

描述 description	;alpha-D-glucopyranuronic acid-(1-3)-beta-D-mannopyranose-(1-4)-alpha-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-4)-[alpha-D-glucopyranuronic acid-(1-3)]beta-D-mannopyranose-(1-4)-alpha-D-glucopyranose-(1-3)-beta-D-glucopyranose ;
分子量 formula_weight	1343.1 kDa
来源方法 src_method	man
拷贝数 entity_count	2

Entity 3 branched

描述 description	alpha-D-glucopyranuronic acid-(1-3)-beta-D-mannopyranose-(1-4)-alpha-D-glucopyranose-(1-3)-beta-D-glucopyranose
分子量 formula_weight	680.6 kDa
来源方法 src_method	man
拷贝数 entity_count	3

Entity 4 non-polymer

描述 description	ACETYL GROUP
分子量 formula_weight	44.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 5 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	18

Entity 6 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	2240

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7. 引用文献 (1)

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晶胞边长 a length_a	204.405 Å
晶胞边长 b length_b	86.357 Å
晶胞边长 c length_c	103.420 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	110.21 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	12

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	monoclinic

分辨率 resolution	1.580 Å
最低分辨率 resolution_low	26.950 Å
R 因子 r_factor	0.1436
R_work r_work	0.1434
R_free r_free	0.1729

fit	/app/data/saxs_computation/iq/8iq9/8iq9.fit
pddf	/app/data/pr_computation/iq/8iq9/8iq9.pr.out
profile	/app/data/saxs_computation/iq/8iq9/8iq9.dat