9ir6

Crystal structure of UDP-N-acetylmuramic Acid L-alanine ligase (MurC) from Roseburia faecis in complex with UNAM

Method: X-RAY DIFFRACTION D_max: 113.1 Å Quality: EXCELLENT

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	9ir6
沉积日期 deposition_date	2024-07-14
结构标题 title	Crystal structure of UDP-N-acetylmuramic Acid L-alanine ligase (MurC) from Roseburia faecis in complex with UNAM
关键词 keywords	MurC, peptidoglycan, UNAM, LIGASE; LIGASE
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	35.06 Å
回转半径 Rg (电子) rg_electron	34.54 Å
零角强度 I(0) i0	163161000.00
分子量 molecular_weight	101930.0 kDa
排除体积 excluded_volume	127320 Å³
包络体积 envelope_volume	163990 Å³
水化壳体积 shell_volume	39804 Å³
包络直径 envelope_diameter	113.2 Å
壳层 Rg shell_rg	40.80 Å
包络 Rg envelope_rg	33.68 Å
形状 Rg shape_rg	34.54 Å
总 Rg total_rg	34.98 Å
总原子数 total_atoms	7168
残基数 n_residues	918
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	113.1 Å
Rg (实空间) rg_real	35.03 Å
Rg 误差 (实空间) rg_real_error	0.97 Å
I(0) (实空间) i0_real	1.6320e+08
I(0) 误差 (实空间) i0_real_error	2.7840e+06
Rg (倒空间) rg_reciprocal	35.05 Å
I(0) (倒空间) i0_reciprocal	163200000.0000
解质量估计 total_estimate	0.9046
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	42.7 Å
偏度 Skewness skewness	0.232
峰度 Kurtosis kurtosis	-0.609
角度范围 angular_range	— – 0.2250 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	23610000.0000
实空间数据点数 n_real_points	46
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.946; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.930

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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-acetylmuramate--L-alanine ligase
分子量 formula_weight	50321.0 kDa
EC 编号 ec_number	6.3.2.8
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	7438

SMYKLKFNDPIHIHFIGIGGISMSGLAEILLEKGFTISGSDAKESDLTRMLASKGAQIFYRQSAENIIPGIDLVVYTAAIHPDNPEFAEARSQGLPMLSRAELLGQIMDNYNNSVAVAGTHGKTTTTSMISEILLAAKSDPTITVGGILPSIGGNLRVGHSGIFVSEACEYTNSFLNFRPKYSIILNVEAEHLDFFKDINDIRRSFRKFAGNTLADGATIINGEIADHQELTDGLPQQIITYGFDDSCEYYADNLTYDDKACPSFTAMHNKEAICEIKLAVPGRHNAGNAMAAIALACTMGISTDAIIRGLDAFHGANRRFQYKGTVDGVTIIDDYAHHPTEIRATLTAAQKYPHKRLVLVFQPHTYSRTKAFLDDFAEVLSMADVIVLADIFAAREQNTFGVSSKDILERLTAKGKDAHYFPSFEEIEKFLLKNCMNGDLLITMGAGNVVEIGESLLGK

来源 Source

来源生物 organism	Roseburia faecis
NCBI 分类编号 ncbi_taxonomy_id	301302
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 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	4

Entity 3 non-polymer

描述 description	;(2R)-2-{[(2R,3R,4R,5S,6R)-3-(acetylamino)-2-{[(S)-{[(R)-{[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-5-hydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-4-yl]oxy}propanoic acid ;
分子量 formula_weight	679.4 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	261

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7. 引用文献 (1)

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晶胞边长 a length_a	74.982 Å
晶胞边长 b length_b	76.688 Å
晶胞边长 c length_c	94.943 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	97.46 °
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	2.430 Å
最低分辨率 resolution_low	47.070 Å
R 因子 r_factor	0.1905
R_work r_work	0.1884
R_free r_free	0.2284

fit	/app/data/saxs_computation/ir/9ir6/9ir6.fit
pddf	/app/data/pr_computation/ir/9ir6/9ir6.pr.out
profile	/app/data/saxs_computation/ir/9ir6/9ir6.dat

Crystal structure of UDP-N-acetylmuramic Acid L-alanine ligase (MurC) from Roseburia faecis in complex with UNAM

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