9ogx

Structure of full-length Streptococcus mutans GtfD active site mutant (D465A, D584A) in complex with sucrose

Method: X-RAY DIFFRACTION D_max: 160.5 Å Quality: REASONABLE

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	9ogx
沉积日期 deposition_date	2025-05-02
最后修订 last_revision	2026-04-22
结构标题 title	Structure of full-length Streptococcus mutans GtfD active site mutant (D465A, D584A) in complex with sucrose
关键词 keywords	GtfD_FL, active site mutant, Dextransucrase, 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	41.02 Å
回转半径 Rg (电子) rg_electron	41.35 Å
零角强度 I(0) i0	302292000.00
分子量 molecular_weight	138040.0 kDa
排除体积 excluded_volume	171130 Å³
包络体积 envelope_volume	238240 Å³
水化壳体积 shell_volume	50698 Å³
包络直径 envelope_diameter	170.2 Å
壳层 Rg shell_rg	43.82 Å
包络 Rg envelope_rg	42.94 Å
形状 Rg shape_rg	41.37 Å
总 Rg total_rg	41.42 Å
总原子数 total_atoms	9753
残基数 n_residues	1237
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	160.5 Å
Rg (实空间) rg_real	41.45 Å
Rg 误差 (实空间) rg_real_error	2.05 Å
I(0) (实空间) i0_real	3.0230e+08
I(0) 误差 (实空间) i0_real_error	5.8700e+06
Rg (倒空间) rg_reciprocal	41.02 Å
I(0) (倒空间) i0_reciprocal	302200000.0000
解质量估计 total_estimate	0.5411
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	41.2 Å
偏度 Skewness skewness	0.738
峰度 Kurtosis kurtosis	0.456
角度范围 angular_range	— – 0.1950 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	39860000.0000
实空间数据点数 n_real_points	40
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.511; Stabil: 1.000; Sysdev: 0.025; Positv: 1.000; Valcen: 0.503; Smooth: 0.920

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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	Glucosyltransferase-S
分子量 formula_weight	160877.1 kDa
EC 编号 ec_number	2.4.1.5
突变 mutation	D465A, D584A
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	9753

MASSVSAETEQQTSDKVVTQKSEDDKAASESSQTDAPKTKQAQTEQTQAQSQANVADTSTSITKETPSQNITTQANSDDKTVTNTKSEEAQTSEERTKQAEEAQATASSQALTQAKAELTKQRQTAAQENKNPVDLAAIPNVKQIDGKYYYIGSDGQPKKNFALTVNNKVLYFDKNTGALTDTSQYQFKQGLTKLNNDYTPHNQIVNFENTSLETIDNYVTADSWYRPKDILKNGKTWTASSESDLRPLLMSWWPDKQTQIAYLNYMNQQGLGTGENYTADSSQESLNLAAQTVQVKIETKISQTQQTQWLRDIINSFVKTQPNWNSQTESDTSAGEKDHLQGGALLYSNSDKTAYANSDYRLLNRTPTSQTGKPKYFEDNSSGGYDFLLANDIDNSNPVVQAEQLNWLHYLMNYGSIVANDPEANFDGVRVAAVDNVNADLLQIASDYLKAHYGVDKSEKNAINHLSILEAWSDNDPQYNKDTKGAQLPIDNKLRLSLLYALTRPLEKDASNKNEIRSGLEPVITNSLNNRSAEGKNSERMANYIFIRAHASEVQTVIAKIIKAQINPKTDGLTFTLDELKQAFKIYNEDMRQAKKKYTQSNIPTAYALMLSNKDSITRLYYGDMYSDDGQYMATKSPYYDAIDTLLKARIKYAAGGQDMKITYVEGDKSHMDWDYTGVLTSVRYGTGANEATDQGSEATKTQGMAVITSNNPSLKLNQNDKVIVNMGTAHKNQEYRPLLLTTKDGLTSYTSDAAAKSLYRKTNDKGELVFDASDIQGYLNPQVSGYLAVWVPVGASDNQDVRVAASNKANATGQVYESSSALDSQLIYEGFSNFQDFVTKDSDYTNKKIAQNVQLFKSWGVTSFEMAPQYVSSEDGSFLDSIIQNGYAFEDRYDLAMSKNNKYGSQQDMINAVKALHKSGIQVIADWVPDQIYNLPGKEVVTATRVNDYGEYRKDSEIKNTLYAANTKSNGKDYQAKYGGAFLSELAAKYPSIFNRTQISNGKKIDPSEKITAWKAKYFNGTNILGRGVGYVLKDNASDKYFELKGNQTYLPKQMTNKEASTGFVNDGNGMTFYSTSGYQAKNSFVQDAKGNWYYFDNNGHMVYGLQHLNGEVQYFLSNGVQLRESFLENADGSKNYFGHLGNRYSNGYYSFDNDSKWRYFDASGVMAVGLKTINGNTQYFDQDGYQVKGAWITGSDGKKRYFDDGSGNMAVNRFANDKNGDWYYLNSDGIALVGVQTINGKTYYFGQDGKQIKGKIITDNGKLKYFLANSGELARNIFATDSQNNWYYFGSDGVAVTGSQTIAGKKLYFASDGKQVKGSFVTYNGKVHYYHADSGELQVNRFEADKDGNWYYLDSNGEALTGSQRINGQRVFFTREGKQVKGDVAYDERGLLRYYDKNSGNMVYNKVVTLANGRRIGIDRWGIARYYLEHHHHHH

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	beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose
分子量 formula_weight	342.3 kDa
来源方法 src_method	man
拷贝数 entity_count	2

Entity 3 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	1

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7. 引用文献 (1)

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晶胞边长 a length_a	83.441 Å
晶胞边长 b length_b	96.993 Å
晶胞边长 c length_c	181.557 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	4

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	2.850 Å
最低分辨率 resolution_low	75.930 Å
R 因子 r_factor	0.2801
R_work r_work	0.2776
R_free r_free	0.3256

fit	/app/data/saxs_computation/og/9ogx/9ogx.fit
pddf	/app/data/pr_computation/og/9ogx/9ogx.pr.out
profile	/app/data/saxs_computation/og/9ogx/9ogx.dat

Structure of full-length Streptococcus mutans GtfD active site mutant (D465A, D584A) in complex with sucrose

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