8e62

;STRUCTURE OF Pcryo_0615 from Psychrobacter cryohalolentis, an N-acetyltransferase required to produce Diacetamido-2,3-dideoxy-D-glucuronic acid ;

Method: X-RAY DIFFRACTION D_max: 111.0 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	8e62
沉积日期 deposition_date	2022-08-22
结构标题 title	;STRUCTURE OF Pcryo_0615 from Psychrobacter cryohalolentis, an N-acetyltransferase required to produce Diacetamido-2,3-dideoxy-D-glucuronic acid ;
关键词 keywords	N-acetyltransferase, 2, 3-diacetamido-2, 3-dideoxy-D-glucuronic acid, Psychrobacter cryohalolentis, 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	34.39 Å
回转半径 Rg (电子) rg_electron	33.96 Å
零角强度 I(0) i0	247994000.00
分子量 molecular_weight	123200.0 kDa
排除体积 excluded_volume	152450 Å³
包络体积 envelope_volume	185100 Å³
水化壳体积 shell_volume	44697 Å³
包络直径 envelope_diameter	116.5 Å
壳层 Rg shell_rg	41.18 Å
包络 Rg envelope_rg	33.86 Å
形状 Rg shape_rg	34.05 Å
总 Rg total_rg	34.15 Å
总原子数 total_atoms	8582
残基数 n_residues	1082
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	111.0 Å
Rg (实空间) rg_real	34.41 Å
Rg 误差 (实空间) rg_real_error	0.72 Å
I(0) (实空间) i0_real	2.4800e+08
I(0) 误差 (实空间) i0_real_error	3.9980e+06
Rg (倒空间) rg_reciprocal	34.40 Å
I(0) (倒空间) i0_reciprocal	248000000.0000
解质量估计 total_estimate	0.8901
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	33.8 Å
偏度 Skewness skewness	0.327
峰度 Kurtosis kurtosis	-0.574
角度范围 angular_range	— – 0.2300 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	91840000.0000
实空间数据点数 n_real_points	47
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.897; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.884

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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	UDP-N-acetylglucosamine acyltransferase
分子量 formula_weight	20516.6 kDa
来源方法 src_method	man
拷贝数 entity_count	6

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F
原子数 atom_count	9286

GGHMNNNAQIHPSAVIHEGVIIEDDVYIGPNCIIGYPPEDKAVFPQTPYTVHICSGTKITGNVTIDAGTIKNTYIGNDCFLMKGAYVAHDVVIGNNVTLSSHVMLGGHVEVMEGANLGMGCIIHQRQKIWHYCMIGMGAIVTKKLVIEPFSIYVGNPAKKIGTNDKGIEKSGIDERAMATIQEEFNARR

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)-4-amino-6-{[(R)-{[(R)-{[(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-hydroxytetrahydro-2H-pyran-2-carboxylic acid ;
分子量 formula_weight	620.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 3 non-polymer

描述 description	COENZYME A
分子量 formula_weight	767.5 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	631

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7. 引用文献 (1)

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晶胞边长 a length_a	82.113 Å
晶胞边长 b length_b	79.768 Å
晶胞边长 c length_c	96.616 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	114.28 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	12

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	—

分辨率 resolution	1.800 Å
最低分辨率 resolution_low	48.150 Å
R 因子 r_factor	0.1680
R_work r_work	0.1659
R_free r_free	0.2081

fit	/app/data/saxs_computation/e6/8e62/8e62.fit
pddf	/app/data/pr_computation/e6/8e62/8e62.pr.out
profile	/app/data/saxs_computation/e6/8e62/8e62.dat

;STRUCTURE OF Pcryo_0615 from Psychrobacter cryohalolentis, an N-acetyltransferase required to produce Diacetamido-2,3-dideoxy-D-glucuronic acid ;

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