8x8g

;Crystal structure of EndoSz mutant D234M, from Streptococcus equi subsp. Zooepidemicus Sz105, in complex with oligosaccharide G2S2-oxazoline ;

Method: X-RAY DIFFRACTION D_max: 120.2 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	8x8g
沉积日期 deposition_date	2023-11-27
结构标题 title	;Crystal structure of EndoSz mutant D234M, from Streptococcus equi subsp. Zooepidemicus Sz105, in complex with oligosaccharide G2S2-oxazoline ;
关键词 keywords	N-linked glycan, glycoside hydrolase, transglycosylation, HYDROLASE, G2S2-oxazoline; 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	39.20 Å
回转半径 Rg (电子) rg_electron	38.72 Å
零角强度 I(0) i0	149045000.00
分子量 molecular_weight	99921.0 kDa
排除体积 excluded_volume	125560 Å³
包络体积 envelope_volume	180610 Å³
水化壳体积 shell_volume	39151 Å³
包络直径 envelope_diameter	129.7 Å
壳层 Rg shell_rg	44.76 Å
包络 Rg envelope_rg	37.47 Å
形状 Rg shape_rg	38.70 Å
总 Rg total_rg	39.19 Å
总原子数 total_atoms	7040
残基数 n_residues	876
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	120.2 Å
Rg (实空间) rg_real	39.18 Å
Rg 误差 (实空间) rg_real_error	1.15 Å
I(0) (实空间) i0_real	1.4900e+08
I(0) 误差 (实空间) i0_real_error	2.7990e+06
Rg (倒空间) rg_reciprocal	39.20 Å
I(0) (倒空间) i0_reciprocal	149000000.0000
解质量估计 total_estimate	0.8697
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	63.1 Å
偏度 Skewness skewness	0.116
峰度 Kurtosis kurtosis	-0.786
角度范围 angular_range	— – 0.2000 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	12430000.0000
实空间数据点数 n_real_points	41
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.902; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.955; Smooth: 0.642

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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	glycoside hydrolase
分子量 formula_weight	107619.5 kDa
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	7334

MVAILAAQHDSLIRVKAEDKLVQTSPSVSAIDALHYLSENSKKEFKEELSKVEKAQPEKLKEIVSKAQQADKQAKTLAEMKVPEKIPMKPLKGPLYGGYFRTWHDKTSDPAEKDKVNSMGELPKEVDLAFVFHDWTKDYSLFWQELATKHVPTLNKQGTRVIRTIPWRFLAGGDHSGIAEDAQKYPNTPEGNKALAKAIVDEYVYKYNLDGLDVMIERDSIPKVNKEESKEGIERSIQVFEEIGKLIGPKGADKSRLFIMDSTYMADKNPLIERGAPYIDLLLVQVYGTQGEKGGFDNANHKAVDTMEERWESYSKYIRPEQYMVGFSFYEEKANSGNLWYDVNVEDDTNPNIGSEIKGTRAERYAKWQPKTGGVKGGIFSYGIDRDGVAHPKKNGPKTPDLDKIVKSDYKVSKALKKVMENDKSYELIDQKDFPDKALREAVIAQVGSRRGNLERFNGTLRLDNPDIKSLEGLNKLKKLAKLELIGLSQITKLDSSVLPENIKPTKDTLVSVLETYKNDDRKEEAKAIPQVALTISGLTGLKELNLAGFDRDSLAGIDAASLTSLEKVDLSSNKLDLAAGTENRQILDTMLATVTKHGGVSEKTFVFDHQKPTGLYPDTYGTKSLQLPVANDTIDLQAKLLFGTVTNQGTLINSEADYKAYQEQEIAGHRFVDSSYDYKAFAVTYKDYKIKVTDSTLGVTDHKDLSTSKEETYKVEFFSPINSTKPVHEAKIVVGEEKTMMVNLAEGATIIGGDADPTNAKKVFDGLLNNDTTTLSTSNKASIIFELKEPGLVKHWRFFNDSKISKADYIKEAKLEAFVGHLEDSSKVKDSLEKSTEWVTVSDYSGEAQEFSQPLNNIGAKYWRITIDNKKSQYGYVSLPELQIIGHRLPEAATVMTTMAAAEELSQQKDKFSQEQLKELEVKVAALKAALDNKMFNADTINASFADVKAYIDKHHHHHH

来源 Source

来源生物 organism	Streptococcus equi subsp. zooepidemicus Sz105
NCBI 分类编号 ncbi_taxonomy_id	1381089
宿主生物 host_organism	Escherichia coli

Entity 2 branched

描述 description	;N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose ;
分子量 formula_weight	1817.6 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 3 non-polymer

描述 description	2-METHYL-4,5-DIHYDRO-(1,2-DIDEOXY-ALPHA-D-GLUCOPYRANOSO)[2,1-D]-1,3-OXAZOLE
分子量 formula_weight	204.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 4 non-polymer

描述 description	CALCIUM ION
分子量 formula_weight	40.1 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

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	294

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7. 引用文献 (1)

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晶胞边长 a length_a	101.061 Å
晶胞边长 b length_b	232.603 Å
晶胞边长 c length_c	50.654 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	2.270 Å
最低分辨率 resolution_low	46.440 Å
R 因子 r_factor	0.2096
R_work r_work	0.2075
R_free r_free	0.2494

fit	/app/data/saxs_computation/x8/8x8g/8x8g.fit
pddf	/app/data/pr_computation/x8/8x8g/8x8g.pr.out
profile	/app/data/saxs_computation/x8/8x8g/8x8g.dat

;Crystal structure of EndoSz mutant D234M, from Streptococcus equi subsp. Zooepidemicus Sz105, in complex with oligosaccharide G2S2-oxazoline ;

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