9nim

Structure of a K1305A mutant of the acyltransferase domain of NcdE, a multi-domain NRPS protein from nocardichelin biosynthesis

Method: X-RAY DIFFRACTION D_max: 52.2 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	9nim
沉积日期 deposition_date	2025-02-26
最后修订 last_revision	2025-07-09
结构标题 title	Structure of a K1305A mutant of the acyltransferase domain of NcdE, a multi-domain NRPS protein from nocardichelin biosynthesis
关键词 keywords	acyltransferase, GNAT, siderophore biosynthesis, NRPS independent siderophores, NcdE-ATx, 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	17.01 Å
回转半径 Rg (电子) rg_electron	15.70 Å
零角强度 I(0) i0	8752190.00
分子量 molecular_weight	21029.0 kDa
排除体积 excluded_volume	26012 Å³
包络体积 envelope_volume	29720 Å³
水化壳体积 shell_volume	15711 Å³
包络直径 envelope_diameter	51.0 Å
壳层 Rg shell_rg	21.83 Å
包络 Rg envelope_rg	15.87 Å
形状 Rg shape_rg	15.71 Å
总 Rg total_rg	16.72 Å
总原子数 total_atoms	2908
残基数 n_residues	186
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	52.2 Å
Rg (实空间) rg_real	16.86 Å
Rg 误差 (实空间) rg_real_error	0.25 Å
I(0) (实空间) i0_real	8.7520e+06
I(0) 误差 (实空间) i0_real_error	9.3340e+04
Rg (倒空间) rg_reciprocal	16.88 Å
I(0) (倒空间) i0_reciprocal	8752000.0000
解质量估计 total_estimate	0.8937
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	23.4 Å
偏度 Skewness skewness	0.031
峰度 Kurtosis kurtosis	-0.477
角度范围 angular_range	— – 0.4700 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	2883000.0000
实空间数据点数 n_real_points	77
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.881; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.992

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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 (3)

Entity 1 polymer

描述 description	NcdE
分子量 formula_weight	22440.1 kDa
EC 编号 ec_number	2.3.1.-
突变 mutation	K1305A
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	3133

GHMAEVGNGATTYHFQSRRIDVDRDLESVHRWLGHPKSHYWDMLNSSLADVEKLIRDAGADPDPRFGMRIGYFEGERQFLFELYNPLTSDLARPGTGYVYETGDIGMHLLVSSSERRLPGFTGAVMLHIMRTAFFEAGARRVVVEPDVRNADVQRLNAAVGFRVAGDFPVPGATARLSYCTREDFARATDNGRTLAGEVES

来源 Source

来源生物 organism	Nocardia carnea
NCBI 分类编号 ncbi_taxonomy_id	1206726
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

描述 description	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
分子量 formula_weight	238.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 3 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	169

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7. 引用文献 (1)

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晶胞边长 a length_a	33.689 Å
晶胞边长 b length_b	69.820 Å
晶胞边长 c length_c	38.140 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	96.51 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	2

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	monoclinic

分辨率 resolution	1.440 Å
最低分辨率 resolution_low	34.910 Å
R 因子 r_factor	0.1652
R_work r_work	0.1638
R_free r_free	0.1916

fit	/app/data/saxs_computation/ni/9nim/9nim.fit
pddf	/app/data/pr_computation/ni/9nim/9nim.pr.out
profile	/app/data/saxs_computation/ni/9nim/9nim.dat

Structure of a K1305A mutant of the acyltransferase domain of NcdE, a multi-domain NRPS protein from nocardichelin biosynthesis

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