8fk4

Structure of the catalytic domain of Streptococcus mutans GtfB complexed to acarbose in orthorhombic space group P21212

Method: X-RAY DIFFRACTION D_max: 289.2 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	8fk4
沉积日期 deposition_date	2022-12-20
结构标题 title	Structure of the catalytic domain of Streptococcus mutans GtfB complexed to acarbose in orthorhombic space group P21212
关键词 keywords	GtfB, GTF-I, insoluble 1, 3-linked alpha glucans, biofilm, streptococcus mutans, glucansucrase, 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	81.40 Å
回转半径 Rg (电子) rg_electron	81.24 Å
零角强度 I(0) i0	8047960000.00
分子量 molecular_weight	746700.0 kDa
排除体积 excluded_volume	927430 Å³
包络体积 envelope_volume	1463500 Å³
水化壳体积 shell_volume	155580 Å³
包络直径 envelope_diameter	265.4 Å
壳层 Rg shell_rg	73.39 Å
包络 Rg envelope_rg	78.44 Å
形状 Rg shape_rg	81.23 Å
总 Rg total_rg	81.20 Å
总原子数 total_atoms	52609
残基数 n_residues	6604
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	289.2 Å
Rg (实空间) rg_real	81.32 Å
Rg 误差 (实空间) rg_real_error	3.65 Å
I(0) (实空间) i0_real	8.0480e+09
I(0) 误差 (实空间) i0_real_error	1.9440e+08
Rg (倒空间) rg_reciprocal	81.32 Å
I(0) (倒空间) i0_reciprocal	8045000000.0000
解质量估计 total_estimate	0.8566
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	121.8 Å
偏度 Skewness skewness	0.112
峰度 Kurtosis kurtosis	-0.707
角度范围 angular_range	— – 0.0950 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	211700000.0000
实空间数据点数 n_real_points	20
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.804; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.729

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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	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	8

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F,G,H
原子数 atom_count	52614

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	man
拷贝数 entity_count	8

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	8

Entity 4 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	41

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	5

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6. 折叠分类 (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

结构域编号 domain_id	8fk4H01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	470 — Glucansucrase

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7. 引用文献 (1)

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晶胞边长 a length_a	299.312 Å
晶胞边长 b length_b	215.766 Å
晶胞边长 c length_c	219.334 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	32

空间群 space_group	P 21 21 2
空间群编号 int_tables_number	18
晶系 crystal_system	—

分辨率 resolution	3.250 Å
最低分辨率 resolution_low	48.882 Å
R 因子 r_factor	0.2252
R_work r_work	0.2236
R_free r_free	0.2551

fit	/app/data/saxs_computation/fk/8fk4/8fk4.fit
pddf	/app/data/pr_computation/fk/8fk4/8fk4.pr.out
profile	/app/data/saxs_computation/fk/8fk4/8fk4.dat