2ae7

Crystal Structure of Human M340H-Beta1,4-Galactosyltransferase-I (M340H-B4GAL-T1) in Complex with Pentasaccharide

Method: X-RAY DIFFRACTION D_max: 123.5 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	2ae7
沉积日期 deposition_date	2005-07-21
结构标题 title	Crystal Structure of Human M340H-Beta1,4-Galactosyltransferase-I (M340H-B4GAL-T1) in Complex with Pentasaccharide
关键词 keywords	beta1, 4-Galactosyltransferase-I; Pentasaccharide; Closed conformation; Mutant, 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	36.34 Å
回转半径 Rg (电子) rg_electron	36.44 Å
零角强度 I(0) i0	157305000.00
分子量 molecular_weight	99058.0 kDa
排除体积 excluded_volume	122860 Å³
包络体积 envelope_volume	150170 Å³
水化壳体积 shell_volume	36544 Å³
包络直径 envelope_diameter	130.4 Å
壳层 Rg shell_rg	39.60 Å
包络 Rg envelope_rg	36.35 Å
形状 Rg shape_rg	36.43 Å
总 Rg total_rg	36.67 Å
总原子数 total_atoms	6942
残基数 n_residues	816
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	123.5 Å
Rg (实空间) rg_real	36.66 Å
Rg 误差 (实空间) rg_real_error	1.24 Å
I(0) (实空间) i0_real	1.5730e+08
I(0) 误差 (实空间) i0_real_error	3.0690e+06
Rg (倒空间) rg_reciprocal	36.47 Å
I(0) (倒空间) i0_reciprocal	157300000.0000
解质量估计 total_estimate	0.8015
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	28.1 Å
偏度 Skewness skewness	0.464
峰度 Kurtosis kurtosis	-0.446
角度范围 angular_range	— – 0.2200 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	81280000.0000
实空间数据点数 n_real_points	45
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.698; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.644; Smooth: 0.677

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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 (9)

Entity 1 polymer

描述 description	Beta-1,4-galactosyltransferase 1
分子量 formula_weight	32773.2 kDa
EC 编号 ec_number	2.4.1.90
突变 mutation	M340H, C338T, R337T
来源方法 src_method	man
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C
原子数 atom_count	7413

ASMTGGQQMGRGSASLPACPEESPLLVGPMLIEFNMPVDLELVAKQNPNVKMGGRYAPRDCVSPHKVAIIIPFRNRQEHLKYWLYYLHPVLQRQQLDYGIYVINQAGDTIFNRAKLLNVGFQEALKDYDYTCFVFSDVDLIPMNDHNAYRCFSQPRHISVAMDKFGFSLPYVQYFGGVSALSKQQFLTINGFPNNYWGWGGEDDDIFNRLVFRGMSISRPNAVVGTTRHIRHSRDKKNEPNPQRFDRIAHTKETMLSDGLNSLTYQVLDVQRYPLYTQITVDIGTPS

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 branched

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose
分子量 formula_weight	383.3 kDa
来源方法 src_method	man
拷贝数 entity_count	2

Entity 3 branched

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose
分子量 formula_weight	545.5 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 4 non-polymer

描述 description	MANGANESE (II) ION
分子量 formula_weight	54.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

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	14

Entity 6 non-polymer

描述 description	6-AMINOHEXYL-URIDINE-C1,5'-DIPHOSPHATE
分子量 formula_weight	503.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 7 non-polymer

描述 description	GLYCEROL
分子量 formula_weight	92.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	7

Entity 8 non-polymer

描述 description	1,4-DIETHYLENE DIOXIDE
分子量 formula_weight	88.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 9 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	471

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6. 折叠分类 (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

结构域编号 domain_id	d2ae7a_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.68 — Nucleotide-diphospho-sugar transferases
超家族 Superfamily superfamily	c.68.1 — Nucleotide-diphospho-sugar transferases
家族 Family family	c.68.1.2 — beta 1,4 galactosyltransferase (b4GalT1)

结构域编号 domain_id	d2ae7b_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.68 — Nucleotide-diphospho-sugar transferases
超家族 Superfamily superfamily	c.68.1 — Nucleotide-diphospho-sugar transferases
家族 Family family	c.68.1.2 — beta 1,4 galactosyltransferase (b4GalT1)

结构域编号 domain_id	d2ae7c_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.68 — Nucleotide-diphospho-sugar transferases
超家族 Superfamily superfamily	c.68.1 — Nucleotide-diphospho-sugar transferases
家族 Family family	c.68.1.2 — beta 1,4 galactosyltransferase (b4GalT1)

CATH v4.4 (3 domains)

结构域编号 domain_id	2ae7A00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	550 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A

结构域编号 domain_id	2ae7B00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	550 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A

结构域编号 domain_id	2ae7C00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	550 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A

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7. 引用文献 (1)

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晶胞边长 a length_a	106.982 Å
晶胞边长 b length_b	195.172 Å
晶胞边长 c length_c	143.919 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	24

空间群 space_group	C 2 2 21
空间群编号 int_tables_number	20
晶系 crystal_system	—

分辨率 resolution	2.000 Å
最低分辨率 resolution_low	40.000 Å
R 因子 r_factor	0.2330
R_work r_work	0.2190
R_free r_free	0.2460

fit	/app/data/saxs_computation/ae/2ae7/2ae7.fit
pddf	/app/data/pr_computation/ae/2ae7/2ae7.pr.out
profile	/app/data/saxs_computation/ae/2ae7/2ae7.dat