8fjc

Structure of the catalytic domain of Streptococcus mutans GtfB complexed to acarbose in tetragonal space group P4322

Method: X-RAY DIFFRACTION D_max: 168.1 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	8fjc
沉积日期 deposition_date	2022-12-19
结构标题 title	Structure of the catalytic domain of Streptococcus mutans GtfB complexed to acarbose in tetragonal space group P4322
关键词 keywords	;GtfB, GTF-I, insoluble 1, 3-linked alpha Glucans, Biofilm, Glucansucrase, inhibitor Acarbose, TRANSFERASE, TRANSFERASE-TRANSFERASE INHIBITOR complex ;; TRANSFERASE/TRANSFERASE INHIBITOR
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	48.18 Å
回转半径 Rg (电子) rg_electron	48.30 Å
零角强度 I(0) i0	607953000.00
分子量 molecular_weight	194120.0 kDa
排除体积 excluded_volume	238660 Å³
包络体积 envelope_volume	305610 Å³
水化壳体积 shell_volume	57484 Å³
包络直径 envelope_diameter	176.5 Å
壳层 Rg shell_rg	46.34 Å
包络 Rg envelope_rg	47.86 Å
形状 Rg shape_rg	48.20 Å
总 Rg total_rg	48.54 Å
总原子数 total_atoms	13603
残基数 n_residues	1678
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	168.1 Å
Rg (实空间) rg_real	48.96 Å
Rg 误差 (实空间) rg_real_error	1.98 Å
I(0) (实空间) i0_real	6.0800e+08
I(0) 误差 (实空间) i0_real_error	1.3500e+07
Rg (倒空间) rg_reciprocal	48.18 Å
I(0) (倒空间) i0_reciprocal	607300000.0000
解质量估计 total_estimate	0.7548
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	35.6 Å
偏度 Skewness skewness	0.578
峰度 Kurtosis kurtosis	-0.432
角度范围 angular_range	— – 0.1650 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	95560000.0000
实空间数据点数 n_real_points	34
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.567; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.655; Smooth: 0.454

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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	Glucosyltransferase-I
分子量 formula_weight	97510.5 kDa
EC 编号 ec_number	2.4.1.5
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	13926

LHFDETGAYTDTSIDTVNKDIVTTRSNLYKKYNQVYDRSAQSFEHVDHYLTAESWYRPKYILKDGKTWTQSTEKDFRPLLMTWWPSQETQRQYVNYMNAQLGINKTYDDTSNQLQLNIAAATIQAKIEAKITTLKNTDWLRQTISAFVKTQSAWNSDSEKPFDDHLQNGAVLYDNEGKLTPYANSNYRILNRTPTNQTGKKDPRYTADNTIGGYEFLLANDVDNSNPVVQAEQLNWLHFLMNFGNIYANDPDANFDSIRVDAVDNVDADLLQIAGDYLKAAKGIHKNDKAANDHLSILEAWSDNDTPYLHDDGDNMINMDNKLRLSLLFSLAKPLNQRSGMNPLITNSLVNRTDDNAETAAVPSYSFIRAHDSEVQDLIRDIIKAEINPNVVGYSFTMEEIKKAFEIYNKDLLATEKKYTHYNTALSYALLLTNKSSVPRVYYGDMFTDDGQYMAHKTINYEAIETLLKARIKYVSGGQAMRNQQVGNSEIITSVRYGKGALKATDTGDRTTRTSGVAVIEGNNPSLRLKASDRVVVNMGAAHKNQAYRPLLLTTDNGIKAYHSDQEAAGLVRYTNDRGELIFTAADIKGYANPQVSGYLGVWVPVGAAADQDVRVAASTAPSTDGKSVHQNAALDSRVMFEGFSNFQAFATKKEEYTNVVIAKNVDKFAEWGVTDFEMAPQYVSSTDGSFLDSVIQNGYAFTDRYDLGISKPNKYGTADDLVKAIKALHSKGIKVMADWVPDQMYAFPEKEVVTATRVDKFGKPVEGSQIKSVLYVADSKSSGKDQQAKYGGAFLEELQAKYPELFARKQISTGVPMDPSVKIKQWSAKYFNGTNILGRGAGYVLKDQATNTYFNISDNKLEHHHHHH

来源 Source

来源生物 organism	Streptococcus mutans
NCBI 分类编号 ncbi_taxonomy_id	1309
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 branched

描述 description	;4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose ;
分子量 formula_weight	645.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 3 non-polymer

描述 description	CALCIUM ION
分子量 formula_weight	40.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 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	8

Entity 5 non-polymer

描述 description	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	51

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	323

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7. 引用文献 (1)

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晶胞边长 a length_a	149.546 Å
晶胞边长 b length_b	149.546 Å
晶胞边长 c length_c	303.085 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	16

空间群 space_group	P 43 2 2
空间群编号 int_tables_number	95
晶系 crystal_system	—

分辨率 resolution	2.500 Å
最低分辨率 resolution_low	83.715 Å
R 因子 r_factor	0.1880
R_work r_work	0.1859
R_free r_free	0.2279

fit	/app/data/saxs_computation/fj/8fjc/8fjc.fit
pddf	/app/data/pr_computation/fj/8fjc/8fjc.pr.out
profile	/app/data/saxs_computation/fj/8fjc/8fjc.dat