SAXSdb — 1f6d

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1f6d
沉积日期 deposition_date	2000-06-21
结构标题 title	THE STRUCTURE OF UDP-N-ACETYLGLUCOSAMINE 2-EPIMERASE FROM E. COLI.
关键词 keywords	sugar-nucleotide epimerase, Rossmann fold, two domains, glycogen phosphorylase superfamily, UDP, dimer, 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	47.99 Å
回转半径 Rg (电子) rg_electron	49.03 Å
零角强度 I(0) i0	443433000.00
分子量 molecular_weight	170920.0 kDa
排除体积 excluded_volume	212400 Å³
包络体积 envelope_volume	293560 Å³
水化壳体积 shell_volume	54065 Å³
包络直径 envelope_diameter	177.8 Å
壳层 Rg shell_rg	46.89 Å
包络 Rg envelope_rg	49.03 Å
形状 Rg shape_rg	49.03 Å
总 Rg total_rg	48.93 Å
总原子数 total_atoms	11880
残基数 n_residues	1451
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	167.4 Å
Rg (实空间) rg_real	48.82 Å
Rg 误差 (实空间) rg_real_error	2.23 Å
I(0) (实空间) i0_real	4.4340e+08
I(0) 误差 (实空间) i0_real_error	9.6090e+06
Rg (倒空间) rg_reciprocal	48.00 Å
I(0) (倒空间) i0_reciprocal	443000000.0000
解质量估计 total_estimate	0.5375
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	40.6 Å
偏度 Skewness skewness	0.636
峰度 Kurtosis kurtosis	-0.146
角度范围 angular_range	— – 0.1650 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	38600000.0000
实空间数据点数 n_real_points	34
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.689; Stabil: 0.999; Sysdev: 0.006; Positv: 1.000; Valcen: 0.711; Smooth: 0.192

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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	UDP-N-ACETYLGLUCOSAMINE 2-EPIMERASE
分子量 formula_weight	42765.4 kDa
EC 编号 ec_number	5.1.3.14
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	12674

MKVLTVFGTRPEAIKMAPLVHALAKDPFFEAKVCVTAQHREMLDQVLKLFSIVPDYDLNIMQPGQGLTEITCRILEGLKPILAEFKPDVVLVHGDTTTTLATSLAAFYQRIPVGHVEAGLRTGDLYSPWPEEANRTLTGHLAMYHFSPTETSRQNLLRENVADSRIFITGNTVIDALLWVRDQVMSSDKLRSELAANYPFIDPDKKMILVTGHRRESFGRGFEEICHALADIATTHQDIQIVYPVHLNPNVREPVNRILGHVKNVILIDPQEYLPFVWLMNHAWLILTDSGGIQEEAPSLGKPVLVMRDTTERPEAVTAGTVRLVGTDKQRIVEEVTRLLKDENEYQAMSRAHNPYGDGQACSRILEALKNNRISL

来源 Source

来源生物 organism	Escherichia coli
NCBI 分类编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	SODIUM ION
分子量 formula_weight	23.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 3 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	4

Entity 4 non-polymer

描述 description	URIDINE-5'-DIPHOSPHATE
分子量 formula_weight	404.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

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	765

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6. 折叠分类 (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1f6da_
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	d1f6db_
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	d1f6dc_
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	d1f6dd_
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 (8 domains)

结构域编号 domain_id	1f6dA01
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	1f6dA02
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	1f6dB01
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	1f6dB02
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	1f6dC01
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	1f6dC02
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	1f6dD01
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	1f6dD02
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	91.008 Å
晶胞边长 b length_b	94.541 Å
晶胞边长 c length_c	100.970 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	109.13 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

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	2.500 Å
最低分辨率 resolution_low	30.320 Å
R 因子 r_factor	0.1980
R_work r_work	0.1980
R_free r_free	0.2710

fit	/app/data/saxs_computation/f6/1f6d/1f6d.fit
pddf	/app/data/pr_computation/f6/1f6d/1f6d.pr.out
profile	/app/data/saxs_computation/f6/1f6d/1f6d.dat

THE STRUCTURE OF UDP-N-ACETYLGLUCOSAMINE 2-EPIMERASE FROM E. COLI.

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution