SAXSdb — 8ip1

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8ip1
沉积日期 deposition_date	2023-03-13
结构标题 title	Escherichia coli OpgD mutant-D388N with beta-1,2-glucan
关键词 keywords	Beta-1, 2-glucanase, 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	34.12 Å
回转半径 Rg (电子) rg_electron	33.95 Å
零角强度 I(0) i0	222725000.00
分子量 molecular_weight	119830.0 kDa
排除体积 excluded_volume	149330 Å³
包络体积 envelope_volume	182670 Å³
水化壳体积 shell_volume	45197 Å³
包络直径 envelope_diameter	122.1 Å
壳层 Rg shell_rg	40.17 Å
包络 Rg envelope_rg	34.21 Å
形状 Rg shape_rg	33.97 Å
总 Rg total_rg	34.31 Å
总原子数 total_atoms	8447
残基数 n_residues	1005
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	113.3 Å
Rg (实空间) rg_real	34.28 Å
Rg 误差 (实空间) rg_real_error	1.07 Å
I(0) (实空间) i0_real	2.2270e+08
I(0) 误差 (实空间) i0_real_error	3.9730e+06
Rg (倒空间) rg_reciprocal	34.18 Å
I(0) (倒空间) i0_reciprocal	222700000.0000
解质量估计 total_estimate	0.8524
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	34.5 Å
偏度 Skewness skewness	0.522
峰度 Kurtosis kurtosis	-0.206
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	103000000.0000
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: 0.808; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.672

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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	63899.9 kDa
突变 mutation	D388N
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	9013

MDRRRFIKGSMAMAAVCGTSGIASLFSQAAFAADSDIADGQTQRFDFSILQSMAHDLAQTAWRGAPRPLPDTLATMTPQAYNSIQYDAEKSLWHNVENRQLDAQFFHMGMGFRRRVRMFSVDPATHLAREIHFRPELFKYNDAGVDTKQLEGQSDLGFAGFRVFKAPELARRDVVSFLGASYFRAVDDTYQYGLSARGLAIDTYTDSKEEFPDFTAFWFDTVKPGATTFTVYALLDSASITGAYKFTIHCEKSQVIMDVENHLYARKDIKQLGIAPMTSMFSCGTNERRMCDTIHPQIHDSDRLSMWRGNGEWICRPLNNPQKLQFNAYTDNNPKGFGLLQLDRDFSHYQDIMGWYNKRPSLWVEPRNKWGKGTIGLMEIPTTGETLNNIVCFWQPEKAVKAGDEFAFQYRLYWSAQPPVHCPLARVMATRTGMGGFSEGWAPGEHYPEKWARRFAVDFVGGDLKAAAPKGIEPVITLSSGEAKQIEILYIEPIDGYRIQFDWYPTSDSTDPVDMRMYLRCQGDAISETWLYQYFPPAPDKRQYVDDRVMSLEHHHHHH

来源 Source

来源生物 organism	Escherichia coli (strain K12)
NCBI 分类编号 ncbi_taxonomy_id	562
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 ;
分子量 formula_weight	1801.6 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-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose ;
分子量 formula_weight	2125.8 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 4 non-polymer

描述 description	DI(HYDROXYETHYL)ETHER
分子量 formula_weight	106.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 5 non-polymer

描述 description	TRIETHYLENE GLYCOL
分子量 formula_weight	150.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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	566

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7. 引用文献 (1)

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晶胞边长 a length_a	58.092 Å
晶胞边长 b length_b	87.099 Å
晶胞边长 c length_c	110.853 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	101.13 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

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	2.060 Å
最低分辨率 resolution_low	47.740 Å
R 因子 r_factor	—
R_work r_work	0.1751
R_free r_free	0.2240

fit	/app/data/saxs_computation/ip/8ip1/8ip1.fit
pddf	/app/data/pr_computation/ip/8ip1/8ip1.pr.out
profile	/app/data/saxs_computation/ip/8ip1/8ip1.dat

Escherichia coli OpgD mutant-D388N 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