SAXSdb — 2c59

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2c59
沉积日期 deposition_date	2005-10-26
结构标题 title	;gdp-mannose-3', 5' -epimerase (arabidopsis thaliana), with gdp-alpha-d-mannose and gdp-beta-l-galactose bound in the active site. ;
关键词 keywords	;3' 5'-EPIMERASE, SHORT CHAIN DEHYDRATASE/REDUCTASE, GDP-MANNOSE, GDP-GULOSE, GDP-GALACTOSE, KETO INTERMEDIATE, VITAMIN C, ASCORBATE BIOSYNTHESIS, ISOMERASE ;; ISOMERASE
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	28.36 Å
回转半径 Rg (电子) rg_electron	27.80 Å
零角强度 I(0) i0	125361000.00
分子量 molecular_weight	85746.0 kDa
排除体积 excluded_volume	105870 Å³
包络体积 envelope_volume	121850 Å³
水化壳体积 shell_volume	36150 Å³
包络直径 envelope_diameter	98.5 Å
壳层 Rg shell_rg	35.63 Å
包络 Rg envelope_rg	28.22 Å
形状 Rg shape_rg	27.81 Å
总 Rg total_rg	28.42 Å
总原子数 total_atoms	6011
残基数 n_residues	726
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	94.4 Å
Rg (实空间) rg_real	28.40 Å
Rg 误差 (实空间) rg_real_error	0.58 Å
I(0) (实空间) i0_real	1.2540e+08
I(0) 误差 (实空间) i0_real_error	1.6230e+06
Rg (倒空间) rg_reciprocal	28.39 Å
I(0) (倒空间) i0_reciprocal	125400000.0000
解质量估计 total_estimate	0.8787
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	30.3 Å
偏度 Skewness skewness	0.406
峰度 Kurtosis kurtosis	-0.318
角度范围 angular_range	— – 0.2800 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	35750000.0000
实空间数据点数 n_real_points	57
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.835; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.939

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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 (7)

Entity 1 polymer

描述 description	;GDP-MANNOSE-3', 5'-EPIMERASE ;
分子量 formula_weight	42943.6 kDa
EC 编号 ec_number	5.1.3.18
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	7048

GAMGTTNGTDYGAYTYKELEREQYWPSENLKISITGAGGFIASHIARRLKHEGHYVIASDWKKNEHMTEDMFCDEFHLVDLRVMENCLKVTEGVDHVFNLAADMGGMGFIQSNHSVIMYNNTMISFNMIEAARINGIKRFFYASSACIYPEFKQLETTNVSLKESDAWPAEPQDAYGLEKLATEELCKHYNKDFGIECRIGRFHNIYGPFGTWKGGREKAPAAFCRKAQTSTDRFEMWGDGLQTRSFTFIDECVEGVLRLTKSDFREPVNIGSDEMVSMNEMAEMVLSFEEKKLPIHHIPGPEGVRGRNSDNNLIKEKLGWAPNMRLKEGLRITYFWIKEQIEKEKAKGSDVSLYGSSKVVGTQAPVQLGSLRAADGKE

来源 Source

来源生物 organism	Arabidopsis thaliana
NCBI 分类编号 ncbi_taxonomy_id	3702
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

描述 description	GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE
分子量 formula_weight	605.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 3 non-polymer

描述 description	GUANOSINE-5'-DIPHOSPHATE-BETA-L-GALACTOSE
分子量 formula_weight	605.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 non-polymer

描述 description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
分子量 formula_weight	663.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 5 non-polymer

描述 description	FORMIC ACID
分子量 formula_weight	46.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	8

Entity 6 non-polymer

描述 description	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
分子量 formula_weight	209.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 7 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	847

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6. 折叠分类 (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d2c59a1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family family	c.2.1.2 — Tyrosine-dependent oxidoreductases

结构域编号 domain_id	d2c59b_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family family	c.2.1.2 — Tyrosine-dependent oxidoreductases

CATH v4.4 (4 domains)

结构域编号 domain_id	2c59A01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

结构域编号 domain_id	2c59A02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	25 — UDP-galactose 4-epimerase; domain 1
同源超家族 H-superfamily homologous superfamily	10 — UDP-galactose 4-epimerase, domain 1

结构域编号 domain_id	2c59B01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

结构域编号 domain_id	2c59B02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	25 — UDP-galactose 4-epimerase; domain 1
同源超家族 H-superfamily homologous superfamily	10 — UDP-galactose 4-epimerase, domain 1

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7. 引用文献 (1)

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晶胞边长 a length_a	62.808 Å
晶胞边长 b length_b	83.812 Å
晶胞边长 c length_c	66.293 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	98.91 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	—

分辨率 resolution	2.000 Å
最低分辨率 resolution_low	29.880 Å
R 因子 r_factor	0.1510
R_work r_work	0.1470
R_free r_free	0.2230

fit	/app/data/saxs_computation/c5/2c59/2c59.fit
pddf	/app/data/pr_computation/c5/2c59/2c59.pr.out
profile	/app/data/saxs_computation/c5/2c59/2c59.dat

;gdp-mannose-3', 5' -epimerase (arabidopsis thaliana), with gdp-alpha-d-mannose and gdp-beta-l-galactose bound in the active site. ;

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution