8e77

;rystal structure of Pcryo_0616, the aminotransferase required to synthesize UDP-N-acetyl-3-amino-D-glucosaminuronic acid (UDP-GlcNAc3NA), incomplete with its external aldimine reaction intermediate ;

Method: X-RAY DIFFRACTION D_max: 72.4 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	8e77
沉积日期 deposition_date	2022-08-23
结构标题 title	;rystal structure of Pcryo_0616, the aminotransferase required to synthesize UDP-N-acetyl-3-amino-D-glucosaminuronic acid (UDP-GlcNAc3NA), incomplete with its external aldimine reaction intermediate ;
关键词 keywords	aminotransferase, Psychrobacter cryohalolentis, carbohydrate, TRANSFERASE; TRANSFERASE
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	21.46 Å
回转半径 Rg (电子) rg_electron	20.49 Å
零角强度 I(0) i0	28569400.00
分子量 molecular_weight	40763.0 kDa
排除体积 excluded_volume	50879 Å³
包络体积 envelope_volume	57944 Å³
水化壳体积 shell_volume	23259 Å³
包络直径 envelope_diameter	73.0 Å
壳层 Rg shell_rg	27.69 Å
包络 Rg envelope_rg	20.92 Å
形状 Rg shape_rg	20.50 Å
总 Rg total_rg	21.35 Å
总原子数 total_atoms	2857
残基数 n_residues	358
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	72.4 Å
Rg (实空间) rg_real	21.38 Å
Rg 误差 (实空间) rg_real_error	0.45 Å
I(0) (实空间) i0_real	2.8570e+07
I(0) 误差 (实空间) i0_real_error	3.5830e+05
Rg (倒空间) rg_reciprocal	21.40 Å
I(0) (倒空间) i0_reciprocal	28570000.0000
解质量估计 total_estimate	0.7984
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	25.6 Å
偏度 Skewness skewness	0.282
峰度 Kurtosis kurtosis	-0.315
角度范围 angular_range	— – 0.3700 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	6875000.0000
实空间数据点数 n_real_points	69
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.793; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.000

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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	DegT/DnrJ/EryC1/StrS aminotransferase
分子量 formula_weight	42013.5 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	3703

MGSSHHHHHHSSENLYFQGGGHMMQFIDLVAQQDRIKDKLNTNIQKVLAHGQYILGPEVHELEEKLSAYTGAKYCITCANGTDALQIAQMVFGIGPGDEVITPGFTYIATAETVAVLGAKPIYVDINPKTYNLDVEQLEAAITPRTKAIIGVSLYGQCADYDAINAIAAKYNIPVIEDAAQSFGASYKGRKSCNLTTIACTSFFPSKPLGCYGDGGAIFTSDEALATVMRQIARHGQDRRYHHIRVGVNSRLDTLQAAILLPKLEILDDEMQVRQRVAETYNQFFIEADITTIPFIESHNQSAWAQYTIQVDNRDEIQAKLREQGIPTAVHYPIPLNKQPAVADTNAVLPVGDEVAERVMSLPMHPYMQTTDIKTICNSF

来源 Source

来源生物 organism	Psychrobacter cryohalolentis K5
NCBI 分类编号 ncbi_taxonomy_id	335284
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

描述 description	;(2S,3S,4R,5R,6R)-5-(acetylamino)-6-{[(R)-{[(S)-{[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-3-hydroxy-4-{[(1E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}tetrahydro-2H-pyran-2-carboxylic acid (non-preferred name) ;
分子量 formula_weight	849.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 3 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	6

Entity 4 non-polymer

描述 description	SODIUM ION
分子量 formula_weight	23.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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	694

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6. 折叠分类 (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

结构域编号 domain_id	8e77A01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	640 — Aspartate Aminotransferase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

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7. 引用文献 (1)

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晶胞边长 a length_a	57.708 Å
晶胞边长 b length_b	96.336 Å
晶胞边长 c length_c	139.467 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	C 2 2 21
空间群编号 int_tables_number	20
晶系 crystal_system	—

分辨率 resolution	1.000 Å
最低分辨率 resolution_low	28.270 Å
R 因子 r_factor	0.1477
R_work r_work	0.1462
R_free r_free	0.1742

fit	/app/data/saxs_computation/e7/8e77/8e77.fit
pddf	/app/data/pr_computation/e7/8e77/8e77.pr.out
profile	/app/data/saxs_computation/e7/8e77/8e77.dat