SAXSdb — 8x18

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8x18
沉积日期 deposition_date	2023-11-06
结构标题 title	Xanthomonas campestris pv. campestris OpgD mutant-D379N with beta-1,2-glucan
关键词 keywords	transglycosylase, 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	35.43 Å
回转半径 Rg (电子) rg_electron	35.60 Å
零角强度 I(0) i0	218713000.00
分子量 molecular_weight	119910.0 kDa
排除体积 excluded_volume	149940 Å³
包络体积 envelope_volume	186200 Å³
水化壳体积 shell_volume	45081 Å³
包络直径 envelope_diameter	127.7 Å
壳层 Rg shell_rg	40.42 Å
包络 Rg envelope_rg	35.62 Å
形状 Rg shape_rg	35.57 Å
总 Rg total_rg	36.01 Å
总原子数 total_atoms	8471
残基数 n_residues	994
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	123.0 Å
Rg (实空间) rg_real	35.69 Å
Rg 误差 (实空间) rg_real_error	1.21 Å
I(0) (实空间) i0_real	2.1870e+08
I(0) 误差 (实空间) i0_real_error	3.5700e+06
Rg (倒空间) rg_reciprocal	35.53 Å
I(0) (倒空间) i0_reciprocal	218700000.0000
解质量估计 total_estimate	0.8354
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	35.5 Å
偏度 Skewness skewness	0.572
峰度 Kurtosis kurtosis	-0.165
角度范围 angular_range	— – 0.2250 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	78230000.0000
实空间数据点数 n_real_points	46
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.723; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.889; Smooth: 0.797

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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	Glucans biosynthesis protein D
分子量 formula_weight	60899.7 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	9012

MQRRHFLKNAAAALAALGLPALPPWALAAKAVGLRRLGQPQPFDYAWLKGQARALAKAPYKSHKQVLPGPLESLNWDQYQSIRYRQDHALWADGNGKFQAKFFHLGLYFHTPVHIYDIVDGKAQQLAYDPAAFDYGRSGLGGKQLPKDLGFAGFRLNTRKDTDRDFSAFLGASYFRAVGKEGQYGQSARGLAIDTGTGGPEEFPDFIAYYLEQPADDSDTVVVYGLLDSPSVSGAYRFAITNGEVLVMDIDSALYPRKAIERLGIGPCTSMYQTGENDRRMDWDWRPEIHDTDGLAMWTGGGEWIWRPLCNPPHLRFNMFVDENPRGFGLLQRDRNFDHYQDDGVFYEKRPCLWVEPKSGWGKGSVQLVEIPTVDETFNNIVAFWNPQAKPQPGQELLMGYRLYWGAHPPASSPLAHCVATRTGLGGIVGQKRSHFSWRFAVDFAGGELAALAKDPKAKVEAVLQVSRGTTEIVSARPLHELKGYRAMFDLVPPDEGTQQIDIRLFLRANGKPLTETWLYQWTPPPASERKIYLEHHHHHH

来源 Source

来源生物 organism	Xanthomonas campestris pv. campestris str. ATCC 33913
NCBI 分类编号 ncbi_taxonomy_id	190485
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 branched

描述 description	;beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose ;
分子量 formula_weight	3585.1 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 3 branched

描述 description	;beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose ;
分子量 formula_weight	1801.6 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 4 branched

描述 description	;beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose ;
分子量 formula_weight	1639.4 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 5 non-polymer

描述 description	GLYCEROL
分子量 formula_weight	92.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	8

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	541

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7. 引用文献 (1)

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晶胞边长 a length_a	171.878 Å
晶胞边长 b length_b	171.878 Å
晶胞边长 c length_c	128.691 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	120.00 °
晶胞分子数 Z z_pdb	12

空间群 space_group	P 65
空间群编号 int_tables_number	170
晶系 crystal_system	—

分辨率 resolution	2.250 Å
最低分辨率 resolution_low	48.723 Å
R 因子 r_factor	—
R_work r_work	0.1726
R_free r_free	0.1761

fit	/app/data/saxs_computation/x1/8x18/8x18.fit
pddf	/app/data/pr_computation/x1/8x18/8x18.pr.out
profile	/app/data/saxs_computation/x1/8x18/8x18.dat

Xanthomonas campestris pv. campestris OpgD mutant-D379N with beta-1,2-glucan

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