1ryw

C115S MurA liganded with reaction products

Method: X-RAY DIFFRACTION D_max: 161.1 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	1ryw
沉积日期 deposition_date	2003-12-22
结构标题 title	C115S MurA liganded with reaction products
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	48.77 Å
回转半径 Rg (电子) rg_electron	48.42 Å
零角强度 I(0) i0	1949840000.00
分子量 molecular_weight	365880.0 kDa
排除体积 excluded_volume	457630 Å³
包络体积 envelope_volume	575650 Å³
水化壳体积 shell_volume	95955 Å³
包络直径 envelope_diameter	158.4 Å
壳层 Rg shell_rg	54.82 Å
包络 Rg envelope_rg	47.48 Å
形状 Rg shape_rg	48.43 Å
总 Rg total_rg	48.55 Å
总原子数 total_atoms	25643
残基数 n_residues	3344
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	161.1 Å
Rg (实空间) rg_real	48.69 Å
Rg 误差 (实空间) rg_real_error	1.37 Å
I(0) (实空间) i0_real	1.9500e+09
I(0) 误差 (实空间) i0_real_error	3.5390e+07
Rg (倒空间) rg_reciprocal	48.77 Å
I(0) (倒空间) i0_reciprocal	1950000000.0000
解质量估计 total_estimate	0.8168
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	55.4 Å
偏度 Skewness skewness	0.278
峰度 Kurtosis kurtosis	-0.550
角度范围 angular_range	— – 0.1600 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	242000000.0000
实空间数据点数 n_real_points	33
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.872; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.000

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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 1-carboxyvinyltransferase
分子量 formula_weight	44813.3 kDa
EC 编号 ec_number	2.5.1.7
突变 mutation	N67D,C115S
来源方法 src_method	man
拷贝数 entity_count	8

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
原子数 atom_count	27527

MDKFRVQGPTRLQGEVTISGAKNAALPILFAALLAEEPVEIQNVPKLKDIDTTMKLLTQLGTKVERDGSVWIDASNVNNFSAPYDLVKTMRASIWALGPLVARFGQGQVSLPGGSAIGARPVDLHIFGLEKLGAEIKLEEGYVKASVNGRLKGAHIVMDKVSVGATVTIMSAATLAEGTTIIENAAREPEIVDTANFLVALGAKISGQGTDRITIEGVERLGGGVYRVLPDRIETGTFLVAAAISGGKIVCRNAQPDTLDAVLAKLREAGADIETGEDWISLDMHGKRPKAVTVRTAPHPAFPTDMQAQFTLLNLVAEGTGVITETIFENRFMHVPELIRMGAHAEIESNTVICHGVEKLSGAQVMATDLRASASLVLAGCIAEGTTVVDRIYHIDRGYERIEDKLRALGANIERVKGE

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

Entity 2 non-polymer

描述 description	PHOSPHATE ION
分子量 formula_weight	95.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	9

Entity 3 non-polymer

描述 description	URIDINE-DIPHOSPHATE-2(N-ACETYLGLUCOSAMINYL) BUTYRIC ACID
分子量 formula_weight	677.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	8

Entity 4 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	17

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	1816

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6. 折叠分类 (SCOP + CATH) 24 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d1rywa_
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	d1rywb_
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	d1rywc_
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	d1rywd_
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	d1rywe_
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	d1rywf_
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	d1rywg_
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	d1rywh_
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 (16 domains)

结构域编号 domain_id	1rywA01
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	1rywA02
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	1rywB01
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	1rywB02
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	1rywC01
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	1rywC02
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	1rywD01
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	1rywD02
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	1rywE01
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	1rywE02
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	1rywF01
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	1rywF02
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	1rywG01
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	1rywG02
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	1rywH01
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	1rywH02
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	80.867 Å
晶胞边长 b length_b	153.729 Å
晶胞边长 c length_c	135.089 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	104.17 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	16

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	2.300 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.1780
R_work r_work	0.1780
R_free r_free	0.2250

fit	/app/data/saxs_computation/ry/1ryw/1ryw.fit
pddf	/app/data/pr_computation/ry/1ryw/1ryw.pr.out
profile	/app/data/saxs_computation/ry/1ryw/1ryw.dat