9egd

AclA from Tenacibaculum discolor in complex with intermediate formed by C8-Lysine attack on ADP

Method: X-RAY DIFFRACTION D_max: 123.5 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	9egd
沉积日期 deposition_date	2024-11-21
结构标题 title	AclA from Tenacibaculum discolor in complex with intermediate formed by C8-Lysine attack on ADP
关键词 keywords	N-acyl-cyclolysine, biosynthesis, signaling, 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	39.89 Å
回转半径 Rg (电子) rg_electron	39.48 Å
零角强度 I(0) i0	1167430000.00
分子量 molecular_weight	188330.0 kDa
排除体积 excluded_volume	182890 Å³
包络体积 envelope_volume	329410 Å³
水化壳体积 shell_volume	66903 Å³
包络直径 envelope_diameter	134.2 Å
壳层 Rg shell_rg	47.24 Å
包络 Rg envelope_rg	39.12 Å
形状 Rg shape_rg	39.49 Å
总 Rg total_rg	39.74 Å
总原子数 total_atoms	14295
残基数 n_residues	1746
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	123.5 Å
Rg (实空间) rg_real	39.60 Å
Rg 误差 (实空间) rg_real_error	0.94 Å
I(0) (实空间) i0_real	1.1670e+09
I(0) 误差 (实空间) i0_real_error	2.1090e+07
Rg (倒空间) rg_reciprocal	39.78 Å
I(0) (倒空间) i0_reciprocal	1168000000.0000
解质量估计 total_estimate	0.9002
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	55.6 Å
偏度 Skewness skewness	0.053
峰度 Kurtosis kurtosis	-0.615
角度范围 angular_range	— – 0.2000 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	263000000.0000
实空间数据点数 n_real_points	41
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.928; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.925

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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	THIF-type NAD/FAD binding fold domain-containing protein
分子量 formula_weight	30056.3 kDa
来源方法 src_method	man
拷贝数 entity_count	7

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F,G
原子数 atom_count	14295

MGSSHHHHHHSQDPMKHRYSRNRLYLNPKEQELIKDYPILLGGAGIGSIIAECALRFGFENITIVDGDHVENSNLNRQNYTEGDVSVNKVEAIKARLKSINSKANIKIHNCFLTSDNVEEYIKGHKVAINALDFSSEVPLLFDEICQKMDIPVLHPYNLGWGGLVTIISPKGLSLNSIAKKGEKFNELNVVEYVSSYMRFWGKPQEWLEDIIYKFKNEREKLSPPQLSVGSWVVAGMCTHILFNIATQREIKSFPEFYLSSLEG

来源 Source

来源生物 organism	Tenacibaculum discolor
NCBI 分类编号 ncbi_taxonomy_id	361581
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	ADENOSINE MONOPHOSPHATE
分子量 formula_weight	347.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	7

Entity 3 non-polymer

描述 description	N~2~-octanoyl-L-lysine
分子量 formula_weight	272.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	7

Entity 4 non-polymer

描述 description	DI(HYDROXYETHYL)ETHER
分子量 formula_weight	106.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

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7. 引用文献 (1)

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晶胞边长 a length_a	204.122 Å
晶胞边长 b length_b	83.875 Å
晶胞边长 c length_c	162.948 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	105.49 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	28

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	3.150 Å
最低分辨率 resolution_low	29.620 Å
R 因子 r_factor	0.1964
R_work r_work	0.1935
R_free r_free	0.2494

fit	/app/data/saxs_computation/eg/9egd/9egd.fit
pddf	/app/data/pr_computation/eg/9egd/9egd.pr.out
profile	/app/data/saxs_computation/eg/9egd/9egd.dat

AclA from Tenacibaculum discolor in complex with intermediate formed by C8-Lysine attack on ADP

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