2bo8

DISSECTION OF MANNOSYLGLYCERATE SYNTHASE: AN ARCHETYPAL MANNOSYLTRANSFERASE

Method: X-RAY DIFFRACTION D_max: 207.1 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	2bo8
沉积日期 deposition_date	2005-04-08
结构标题 title	DISSECTION OF MANNOSYLGLYCERATE SYNTHASE: AN ARCHETYPAL MANNOSYLTRANSFERASE
关键词 keywords	CATALYSIS, GLYCOSYLTRANSFERASE, MANNOSE, TRANSFERASE, STEREOSELECTIVITY; 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	64.18 Å
回转半径 Rg (电子) rg_electron	64.96 Å
零角强度 I(0) i0	2942810000.00
分子量 molecular_weight	450910.0 kDa
排除体积 excluded_volume	560870 Å³
包络体积 envelope_volume	764960 Å³
水化壳体积 shell_volume	103720 Å³
包络直径 envelope_diameter	232.7 Å
壳层 Rg shell_rg	59.37 Å
包络 Rg envelope_rg	63.88 Å
形状 Rg shape_rg	64.97 Å
总 Rg total_rg	64.81 Å
总原子数 total_atoms	31790
残基数 n_residues	3810
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	207.1 Å
Rg (实空间) rg_real	64.86 Å
Rg 误差 (实空间) rg_real_error	1.68 Å
I(0) (实空间) i0_real	2.9420e+09
I(0) 误差 (实空间) i0_real_error	6.1720e+07
Rg (倒空间) rg_reciprocal	63.50 Å
I(0) (倒空间) i0_reciprocal	2936000000.0000
解质量估计 total_estimate	0.8287
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	60.4 Å
偏度 Skewness skewness	0.544
峰度 Kurtosis kurtosis	-0.286
角度范围 angular_range	— – 0.1200 Å⁻¹
当前正则化参数 α current_alpha	0.0005
最高正则化参数 α highest_alpha	111300000.0000
实空间数据点数 n_real_points	25
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.880; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.147

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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	MANNOSYLGLYCERATE SYNTHASE
分子量 formula_weight	46186.5 kDa
EC 编号 ec_number	2.4.1.-
来源方法 src_method	man
拷贝数 entity_count	10

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,I,J
原子数 atom_count	32098

MSLVVFPFKHEHPEVLLHNVRVAAAHPRVHEVLCIGYERDQTYEAVERAAPEISRATGTPVSVRLQERLGTLRPGKGDGMNTALRYFLEETQWERIHFYDADITSFGPDWITKAEEAADFGYGLVRHYFPRASTDAMITWMITRTGFALLWPHTELSWIEQPLGGELLMRREVAAMLYEDERVRRRSDWGIDTLYTFVTVQQGVSIYECYIPEGKAHRLYGGLDDLRTMLVECFAAIQSLQHEVVGQPAIHRQEHPHRVPVHIAERVGYDVEATLHRLMQHWTPRQVELLELFTTPVREGLRTCQRRPAFNFMDEMAWAATYHVLLEHFQPGDPDWEELLFKLWTTRVLNYTMTVALRGYDYAQQYLYRMLGRYRYQAALENGRGHPVPPRAALSTA

来源 Source

来源生物 organism	RHODOTHERMUS MARINUS
NCBI 分类编号 ncbi_taxonomy_id	29549
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 non-polymer

描述 description	;GUANOSINE 5'-(TRIHYDROGEN DIPHOSPHATE), P'-D-MANNOPYRANOSYL ESTER ;
分子量 formula_weight	619.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	10

Entity 3 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	10

Entity 4 non-polymer

描述 description	CHLORIDE ION
分子量 formula_weight	35.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	10

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	308

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6. 折叠分类 (SCOP + CATH) 20 domains

SCOP 2.08 (10 domains)

结构域编号 domain_id	d2bo8a_
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.68.1.18 — MGS-like

结构域编号 domain_id	d2bo8b_
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.68.1.18 — MGS-like

结构域编号 domain_id	d2bo8c_
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.68.1.18 — MGS-like

结构域编号 domain_id	d2bo8d_
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.68.1.18 — MGS-like

结构域编号 domain_id	d2bo8e_
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.68.1.18 — MGS-like

结构域编号 domain_id	d2bo8f_
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.68.1.18 — MGS-like

结构域编号 domain_id	d2bo8g_
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.68.1.18 — MGS-like

结构域编号 domain_id	d2bo8h_
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.68.1.18 — MGS-like

结构域编号 domain_id	d2bo8i_
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.68.1.18 — MGS-like

结构域编号 domain_id	d2bo8j_
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.68.1.18 — MGS-like

CATH v4.4 (10 domains)

结构域编号 domain_id	2bo8A01
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	2bo8B01
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	2bo8C01
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	2bo8D01
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	2bo8E01
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	2bo8F01
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	2bo8G01
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	2bo8H01
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	2bo8I01
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	2bo8J01
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	405.094 Å
晶胞边长 b length_b	161.430 Å
晶胞边长 c length_c	108.708 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	40

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	2.800 Å
最低分辨率 resolution_low	74.120 Å
R 因子 r_factor	0.1960
R_work r_work	0.1950
R_free r_free	0.2160

fit	/app/data/saxs_computation/bo/2bo8/2bo8.fit
pddf	/app/data/pr_computation/bo/2bo8/2bo8.pr.out
profile	/app/data/saxs_computation/bo/2bo8/2bo8.dat