8j30

Crystal structure of ApNGT with Q469A and M218A mutations in complex with UDP-GLC

Method: X-RAY DIFFRACTION D_max: 121.9 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	8j30
沉积日期 deposition_date	2023-04-15
结构标题 title	Crystal structure of ApNGT with Q469A and M218A mutations in complex with UDP-GLC
关键词 keywords	Actinobacillus pleuropneumoniae, N-glycosyltransferase, 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	36.90 Å
回转半径 Rg (电子) rg_electron	36.41 Å
零角强度 I(0) i0	282698000.00
分子量 molecular_weight	137450.0 kDa
排除体积 excluded_volume	172210 Å³
包络体积 envelope_volume	215720 Å³
水化壳体积 shell_volume	48098 Å³
包络直径 envelope_diameter	125.3 Å
壳层 Rg shell_rg	43.77 Å
包络 Rg envelope_rg	36.04 Å
形状 Rg shape_rg	36.42 Å
总 Rg total_rg	36.86 Å
总原子数 total_atoms	9688
残基数 n_residues	1204
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	121.9 Å
Rg (实空间) rg_real	36.85 Å
Rg 误差 (实空间) rg_real_error	1.21 Å
I(0) (实空间) i0_real	2.8270e+08
I(0) 误差 (实空间) i0_real_error	5.0500e+06
Rg (倒空间) rg_reciprocal	36.89 Å
I(0) (倒空间) i0_reciprocal	282700000.0000
解质量估计 total_estimate	0.8912
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	0
主峰位置 r_peak_primary	— Å
偏度 Skewness skewness	0.262
峰度 Kurtosis kurtosis	-0.449
角度范围 angular_range	— – 0.2150 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	66840000.0000
实空间数据点数 n_real_points	44
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.902; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.892

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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	UDP-glucose:protein N-beta-glucosyltransferase
分子量 formula_weight	71532.2 kDa
EC 编号 ec_number	2.4.1.-
突变 mutation	Q469A,M218A
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	9688

MENENKPNVANFEAAVAAKDYEKACSELLLILSQLDSNFGGIHEIEFEYPAQLQDLEQEKIVYFCTRMATAITTLFSDPVLEISDLGVQRFLVYQRWLALIFASSPFVNADHILQTYNREPNRKNSLEIHLDSSKSSLIKFCILYLPESNVNLNLDVMWNISPELCASLCFALQSPRFVGTSTAFNKRATILQWFPRHLDQLKNLNNIPSAISHDVYAHCSYDTSVNKHDVKRALNHVIRRHIESEYGWKDRDVAHIGYRNNKPVMVVLLEHFHSAHSIYRTHSTSMIAAREHFYLIGLGSPSVDQAGQEVFDEFHLVAGDNMKQKLEFIRSVCESNGAAIFYMPSIGMDMTTIFASNTRLAPIQAIALGHPATTHSDFIEYVIVEDDYVGSEECFSETLLRLPKDALPYVPSALAPEKVDYLLRENPEVVNIGIASTTMKLNPYFLEALKAIRDRAKVKVHFHFALGASNGITHPYVERFIKSYLGDSATAHPHSPYHQYLRILHNCDMMVNPFPFGNTNGIIDMVTLGLVGVCKTGAEVHEHIDEGLFKRLGLPEWLIANTVDEYVERAVRLAENHQERLELRRYIIENNGLNTLFTGDPRPMGQVFLEKLNAFLKENLEHHHHHH

来源 Source

来源生物 organism	Actinobacillus pleuropneumoniae serovar 5b str. L20
NCBI 分类编号 ncbi_taxonomy_id	416269
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	URIDINE-5'-DIPHOSPHATE-GLUCOSE
分子量 formula_weight	566.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 3 non-polymer

描述 description	URIDINE-5'-DIPHOSPHATE
分子量 formula_weight	404.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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7. 引用文献 (1)

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晶胞边长 a length_a	79.409 Å
晶胞边长 b length_b	95.011 Å
晶胞边长 c length_c	175.974 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	2.890 Å
最低分辨率 resolution_low	47.180 Å
R 因子 r_factor	0.2134
R_work r_work	0.2114
R_free r_free	0.2497

fit	/app/data/saxs_computation/j3/8j30/8j30.fit
pddf	/app/data/pr_computation/j3/8j30/8j30.pr.out
profile	/app/data/saxs_computation/j3/8j30/8j30.dat

Crystal structure of ApNGT with Q469A and M218A mutations in complex with UDP-GLC

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