SAXSdb — 1v4v

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1v4v
沉积日期 deposition_date	2003-11-19
结构标题 title	Crystal Structure Of UDP-N-Acetylglucosamine 2-Epimerase From Thermus Thermophilus HB8
关键词 keywords	UDP-GlcNAc, Two Domains, Homodimer, RIKEN Structural Genomics/Proteomics Initiative, RSGI, Structural Genomics, 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	33.78 Å
回转半径 Rg (电子) rg_electron	34.03 Å
零角强度 I(0) i0	102084000.00
分子量 molecular_weight	82184.0 kDa
排除体积 excluded_volume	103510 Å³
包络体积 envelope_volume	133420 Å³
水化壳体积 shell_volume	35661 Å³
包络直径 envelope_diameter	127.5 Å
壳层 Rg shell_rg	37.28 Å
包络 Rg envelope_rg	33.96 Å
形状 Rg shape_rg	34.04 Å
总 Rg total_rg	34.24 Å
总原子数 total_atoms	5730
残基数 n_residues	727
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	120.7 Å
Rg (实空间) rg_real	34.11 Å
Rg 误差 (实空间) rg_real_error	1.30 Å
I(0) (实空间) i0_real	1.0210e+08
I(0) 误差 (实空间) i0_real_error	1.8080e+06
Rg (倒空间) rg_reciprocal	33.90 Å
I(0) (倒空间) i0_reciprocal	102100000.0000
解质量估计 total_estimate	0.7938
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	30.8 Å
偏度 Skewness skewness	0.632
峰度 Kurtosis kurtosis	-0.039
角度范围 angular_range	— – 0.2350 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	32990000.0000
实空间数据点数 n_real_points	48
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.670; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.580; Smooth: 0.726

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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 (4)

Entity 1 polymer

描述 description	UDP-N-Acetylglucosamine 2-Epimerase
分子量 formula_weight	41402.5 kDa
EC 编号 ec_number	5.1.3.14
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	6736

MEGGMKRVVLAFGTRPEATKMAPVYLALRGIPGLKPLVLLTGQHREQLRQALSLFGIQEDRNLDVMQERQALPDLAARILPQAARALKEMGADYVLVHGDTLTTFAVAWAAFLEGIPVGHVEAGLRSGNLKEPFPEEANRRLTDVLTDLDFAPTPLAKANLLKEGKREEGILVTGQTGVDAVLLAAKLGRLPEGLPEGPYVTVTMHRRENWPLLSDLAQALKRVAEAFPHLTFVYPVHLNPVVREAVFPVLKGVRNFVLLDPLEYGSMAALMRASLLLVTDSGGLQEEGAALGVPVVVLRNVTERPEGLKAGILKLAGTDPEGVYRVVKGLLENPEELSRMRKAKNPYGDGKAGLMVARGVAWRLGLGPRPEDWLP

来源 Source

来源生物 organism	Thermus thermophilus
NCBI 分类编号 ncbi_taxonomy_id	274
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

描述 description	ACETIC ACID
分子量 formula_weight	60.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 3 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	2

Entity 4 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	974

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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	d1v4va_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.87 — UDP-Glycosyltransferase/glycogen phosphorylase
超家族 Superfamily superfamily	c.87.1 — UDP-Glycosyltransferase/glycogen phosphorylase
家族 Family family	c.87.1.3 — UDP-N-acetylglucosamine 2-epimerase

结构域编号 domain_id	d1v4vb_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.87 — UDP-Glycosyltransferase/glycogen phosphorylase
超家族 Superfamily superfamily	c.87.1 — UDP-Glycosyltransferase/glycogen phosphorylase
家族 Family family	c.87.1.3 — UDP-N-acetylglucosamine 2-epimerase

CATH v4.4 (4 domains)

结构域编号 domain_id	1v4vA01
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	2000 — Glycogen Phosphorylase B;

结构域编号 domain_id	1v4vA02
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	2000 — Glycogen Phosphorylase B;

结构域编号 domain_id	1v4vB01
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	2000 — Glycogen Phosphorylase B;

结构域编号 domain_id	1v4vB02
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	2000 — Glycogen Phosphorylase B;

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7. 引用文献 (1)

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晶胞边长 a length_a	169.728 Å
晶胞边长 b length_b	51.448 Å
晶胞边长 c length_c	105.506 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	104.20 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	—

分辨率 resolution	1.800 Å
最低分辨率 resolution_low	40.000 Å
R 因子 r_factor	—
R_work r_work	0.2090
R_free r_free	0.2350

fit	/app/data/saxs_computation/v4/1v4v/1v4v.fit
pddf	/app/data/pr_computation/v4/1v4v/1v4v.pr.out
profile	/app/data/saxs_computation/v4/1v4v/1v4v.dat

Crystal Structure Of UDP-N-Acetylglucosamine 2-Epimerase From Thermus Thermophilus HB8

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