1q3g

MurA (Asp305Ala) liganded with tetrahedral reaction intermediate

Method: X-RAY DIFFRACTION D_max: 221.1 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	1q3g
沉积日期 deposition_date	2003-07-29
结构标题 title	MurA (Asp305Ala) liganded with tetrahedral reaction intermediate
关键词 keywords	inside-out alpha-beta barrel, 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	64.39 Å
回转半径 Rg (电子) rg_electron	64.22 Å
零角强度 I(0) i0	7507730000.00
分子量 molecular_weight	729060.0 kDa
排除体积 excluded_volume	912440 Å³
包络体积 envelope_volume	1215100 Å³
水化壳体积 shell_volume	154390 Å³
包络直径 envelope_diameter	222.0 Å
壳层 Rg shell_rg	68.20 Å
包络 Rg envelope_rg	62.52 Å
形状 Rg shape_rg	64.23 Å
总 Rg total_rg	64.22 Å
总原子数 total_atoms	51088
残基数 n_residues	6688
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	221.1 Å
Rg (实空间) rg_real	64.35 Å
Rg 误差 (实空间) rg_real_error	2.08 Å
I(0) (实空间) i0_real	7.5080e+09
I(0) 误差 (实空间) i0_real_error	1.6410e+08
Rg (倒空间) rg_reciprocal	64.40 Å
I(0) (倒空间) i0_reciprocal	7508000000.0000
解质量估计 total_estimate	0.8564
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	82.9 Å
偏度 Skewness skewness	0.322
峰度 Kurtosis kurtosis	-0.320
角度范围 angular_range	— – 0.1200 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	1880000000.0000
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: 0.830; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.644

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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 1-carboxyvinyltransferase
分子量 formula_weight	44785.4 kDa
EC 编号 ec_number	2.5.1.7
突变 mutation	N67D,D305A
来源方法 src_method	man
拷贝数 entity_count	16

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,K,L,W,X,Y,Z
原子数 atom_count	52519

MDKFRVQGPTRLQGEVTISGAKNAALPILFAALLAEEPVEIQNVPKLKDIDTTMKLLTQLGTKVERDGSVWIDASNVNNFSAPYDLVKTMRASIWALGPLVARFGQGQVSLPGGCAIGARPVDLHIFGLEKLGAEIKLEEGYVKASVNGRLKGAHIVMDKVSVGATVTIMSAATLAEGTTIIENAAREPEIVDTANFLVALGAKISGQGTDRITIEGVERLGGGVYRVLPDRIETGTFLVAAAISGGKIVCRNAQPDTLDAVLAKLREAGADIETGEDWISLDMHGKRPKAVTVRTAPHPAFPTAMQAQFTLLNLVAEGTGVITETIFENRFMHVPELIRMGAHAEIESNTVICHGVEKLSGAQVMATDLRASASLVLAGCIAEGTTVVDRIYHIDRGYERIEDKLRALGANIERVKGE

来源 Source

来源生物 organism	Enterobacter cloacae
NCBI 分类编号 ncbi_taxonomy_id	550
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

描述 description	3'-1-CARBOXY-1-PHOSPHONOOXY-ETHOXY-URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE
分子量 formula_weight	775.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	16

Entity 3 non-polymer

描述 description	1,2-ETHANEDIOL
分子量 formula_weight	62.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	16

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	1431

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6. 折叠分类 (SCOP + CATH) 48 domains

SCOP 2.08 (16 domains)

结构域编号 domain_id	d1q3ga_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.68 — IF3-like
超家族 Superfamily superfamily	d.68.2 — EPT/RTPC-like
家族 Family family	d.68.2.2 — Enolpyruvate transferase, EPT

结构域编号 domain_id	d1q3gb_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.68 — IF3-like
超家族 Superfamily superfamily	d.68.2 — EPT/RTPC-like
家族 Family family	d.68.2.2 — Enolpyruvate transferase, EPT

结构域编号 domain_id	d1q3gc_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.68 — IF3-like
超家族 Superfamily superfamily	d.68.2 — EPT/RTPC-like
家族 Family family	d.68.2.2 — Enolpyruvate transferase, EPT

结构域编号 domain_id	d1q3gd_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.68 — IF3-like
超家族 Superfamily superfamily	d.68.2 — EPT/RTPC-like
家族 Family family	d.68.2.2 — Enolpyruvate transferase, EPT

结构域编号 domain_id	d1q3ge_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.68 — IF3-like
超家族 Superfamily superfamily	d.68.2 — EPT/RTPC-like
家族 Family family	d.68.2.2 — Enolpyruvate transferase, EPT

结构域编号 domain_id	d1q3gf_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.68 — IF3-like
超家族 Superfamily superfamily	d.68.2 — EPT/RTPC-like
家族 Family family	d.68.2.2 — Enolpyruvate transferase, EPT

结构域编号 domain_id	d1q3gg_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.68 — IF3-like
超家族 Superfamily superfamily	d.68.2 — EPT/RTPC-like
家族 Family family	d.68.2.2 — Enolpyruvate transferase, EPT

结构域编号 domain_id	d1q3gh_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.68 — IF3-like
超家族 Superfamily superfamily	d.68.2 — EPT/RTPC-like
家族 Family family	d.68.2.2 — Enolpyruvate transferase, EPT

结构域编号 domain_id	d1q3gi_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.68 — IF3-like
超家族 Superfamily superfamily	d.68.2 — EPT/RTPC-like
家族 Family family	d.68.2.2 — Enolpyruvate transferase, EPT

结构域编号 domain_id	d1q3gj_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.68 — IF3-like
超家族 Superfamily superfamily	d.68.2 — EPT/RTPC-like
家族 Family family	d.68.2.2 — Enolpyruvate transferase, EPT

结构域编号 domain_id	d1q3gk_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.68 — IF3-like
超家族 Superfamily superfamily	d.68.2 — EPT/RTPC-like
家族 Family family	d.68.2.2 — Enolpyruvate transferase, EPT

结构域编号 domain_id	d1q3gl_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.68 — IF3-like
超家族 Superfamily superfamily	d.68.2 — EPT/RTPC-like
家族 Family family	d.68.2.2 — Enolpyruvate transferase, EPT

结构域编号 domain_id	d1q3gw_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.68 — IF3-like
超家族 Superfamily superfamily	d.68.2 — EPT/RTPC-like
家族 Family family	d.68.2.2 — Enolpyruvate transferase, EPT

结构域编号 domain_id	d1q3gx_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.68 — IF3-like
超家族 Superfamily superfamily	d.68.2 — EPT/RTPC-like
家族 Family family	d.68.2.2 — Enolpyruvate transferase, EPT

结构域编号 domain_id	d1q3gy_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.68 — IF3-like
超家族 Superfamily superfamily	d.68.2 — EPT/RTPC-like
家族 Family family	d.68.2.2 — Enolpyruvate transferase, EPT

结构域编号 domain_id	d1q3gz_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.68 — IF3-like
超家族 Superfamily superfamily	d.68.2 — EPT/RTPC-like
家族 Family family	d.68.2.2 — Enolpyruvate transferase, EPT

CATH v4.4 (32 domains)

结构域编号 domain_id	1q3gA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	65 — Alpha-beta prism
拓扑 Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
同源超家族 H-superfamily homologous superfamily	10 — Enolpyruvate transferase domain

结构域编号 domain_id	1q3gA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	65 — Alpha-beta prism
拓扑 Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
同源超家族 H-superfamily homologous superfamily	10 — Enolpyruvate transferase domain

结构域编号 domain_id	1q3gB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	65 — Alpha-beta prism
拓扑 Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
同源超家族 H-superfamily homologous superfamily	10 — Enolpyruvate transferase domain

结构域编号 domain_id	1q3gB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	65 — Alpha-beta prism
拓扑 Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
同源超家族 H-superfamily homologous superfamily	10 — Enolpyruvate transferase domain

结构域编号 domain_id	1q3gC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	65 — Alpha-beta prism
拓扑 Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
同源超家族 H-superfamily homologous superfamily	10 — Enolpyruvate transferase domain

结构域编号 domain_id	1q3gC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	65 — Alpha-beta prism
拓扑 Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
同源超家族 H-superfamily homologous superfamily	10 — Enolpyruvate transferase domain

结构域编号 domain_id	1q3gD01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	65 — Alpha-beta prism
拓扑 Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
同源超家族 H-superfamily homologous superfamily	10 — Enolpyruvate transferase domain

结构域编号 domain_id	1q3gD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	65 — Alpha-beta prism
拓扑 Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
同源超家族 H-superfamily homologous superfamily	10 — Enolpyruvate transferase domain

结构域编号 domain_id	1q3gE01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	65 — Alpha-beta prism
拓扑 Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
同源超家族 H-superfamily homologous superfamily	10 — Enolpyruvate transferase domain

结构域编号 domain_id	1q3gE02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	65 — Alpha-beta prism
拓扑 Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
同源超家族 H-superfamily homologous superfamily	10 — Enolpyruvate transferase domain

结构域编号 domain_id	1q3gF01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	65 — Alpha-beta prism
拓扑 Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
同源超家族 H-superfamily homologous superfamily	10 — Enolpyruvate transferase domain

结构域编号 domain_id	1q3gF02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	65 — Alpha-beta prism
拓扑 Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
同源超家族 H-superfamily homologous superfamily	10 — Enolpyruvate transferase domain

结构域编号 domain_id	1q3gG01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	65 — Alpha-beta prism
拓扑 Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
同源超家族 H-superfamily homologous superfamily	10 — Enolpyruvate transferase domain

结构域编号 domain_id	1q3gG02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	65 — Alpha-beta prism
拓扑 Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
同源超家族 H-superfamily homologous superfamily	10 — Enolpyruvate transferase domain

结构域编号 domain_id	1q3gH01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	65 — Alpha-beta prism
拓扑 Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
同源超家族 H-superfamily homologous superfamily	10 — Enolpyruvate transferase domain

结构域编号 domain_id	1q3gH02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	65 — Alpha-beta prism
拓扑 Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
同源超家族 H-superfamily homologous superfamily	10 — Enolpyruvate transferase domain

结构域编号 domain_id	1q3gI01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	65 — Alpha-beta prism
拓扑 Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
同源超家族 H-superfamily homologous superfamily	10 — Enolpyruvate transferase domain

结构域编号 domain_id	1q3gI02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	65 — Alpha-beta prism
拓扑 Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
同源超家族 H-superfamily homologous superfamily	10 — Enolpyruvate transferase domain

结构域编号 domain_id	1q3gJ01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	65 — Alpha-beta prism
拓扑 Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
同源超家族 H-superfamily homologous superfamily	10 — Enolpyruvate transferase domain

结构域编号 domain_id	1q3gJ02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	65 — Alpha-beta prism
拓扑 Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
同源超家族 H-superfamily homologous superfamily	10 — Enolpyruvate transferase domain

结构域编号 domain_id	1q3gK01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	65 — Alpha-beta prism
拓扑 Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
同源超家族 H-superfamily homologous superfamily	10 — Enolpyruvate transferase domain

结构域编号 domain_id	1q3gK02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	65 — Alpha-beta prism
拓扑 Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
同源超家族 H-superfamily homologous superfamily	10 — Enolpyruvate transferase domain

结构域编号 domain_id	1q3gL01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	65 — Alpha-beta prism
拓扑 Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
同源超家族 H-superfamily homologous superfamily	10 — Enolpyruvate transferase domain

结构域编号 domain_id	1q3gL02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	65 — Alpha-beta prism
拓扑 Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
同源超家族 H-superfamily homologous superfamily	10 — Enolpyruvate transferase domain

结构域编号 domain_id	1q3gW01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	65 — Alpha-beta prism
拓扑 Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
同源超家族 H-superfamily homologous superfamily	10 — Enolpyruvate transferase domain

结构域编号 domain_id	1q3gW02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	65 — Alpha-beta prism
拓扑 Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
同源超家族 H-superfamily homologous superfamily	10 — Enolpyruvate transferase domain

结构域编号 domain_id	1q3gX01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	65 — Alpha-beta prism
拓扑 Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
同源超家族 H-superfamily homologous superfamily	10 — Enolpyruvate transferase domain

结构域编号 domain_id	1q3gX02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	65 — Alpha-beta prism
拓扑 Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
同源超家族 H-superfamily homologous superfamily	10 — Enolpyruvate transferase domain

结构域编号 domain_id	1q3gY01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	65 — Alpha-beta prism
拓扑 Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
同源超家族 H-superfamily homologous superfamily	10 — Enolpyruvate transferase domain

结构域编号 domain_id	1q3gY02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	65 — Alpha-beta prism
拓扑 Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
同源超家族 H-superfamily homologous superfamily	10 — Enolpyruvate transferase domain

结构域编号 domain_id	1q3gZ01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	65 — Alpha-beta prism
拓扑 Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
同源超家族 H-superfamily homologous superfamily	10 — Enolpyruvate transferase domain

结构域编号 domain_id	1q3gZ02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	65 — Alpha-beta prism
拓扑 Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
同源超家族 H-superfamily homologous superfamily	10 — Enolpyruvate transferase domain

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7. 引用文献 (1)

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晶胞边长 a length_a	139.459 Å
晶胞边长 b length_b	153.934 Å
晶胞边长 c length_c	167.481 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	112.95 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	32

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	2.650 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.2170
R_work r_work	0.2170
R_free r_free	0.2530