9i4j

X-ray structure of the drug binding domain of AlbA in complex with the KMR-04-161 compound of the pyrrolobenzodiazepines class

Method: X-RAY DIFFRACTION D_max: 61.8 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	9i4j
沉积日期 deposition_date	2025-01-24
最后修订 last_revision	2026-02-04
结构标题 title	X-ray structure of the drug binding domain of AlbA in complex with the KMR-04-161 compound of the pyrrolobenzodiazepines class
关键词 keywords	DRUG BINDING, BACTERIAL RESISTANCE, PYRROLOBENZODIAZEPINES, DNA BINDING PROTEIN, ANTIMICROBIAL PROTEIN; ANTIMICROBIAL PROTEIN
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	19.33 Å
回转半径 Rg (电子) rg_electron	18.32 Å
零角强度 I(0) i0	24532500.00
分子量 molecular_weight	25184.0 kDa
排除体积 excluded_volume	24269 Å³
包络体积 envelope_volume	38724 Å³
水化壳体积 shell_volume	17816 Å³
包络直径 envelope_diameter	60.4 Å
壳层 Rg shell_rg	24.40 Å
包络 Rg envelope_rg	18.60 Å
形状 Rg shape_rg	18.29 Å
总 Rg total_rg	19.05 Å
总原子数 total_atoms	1902
残基数 n_residues	216
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	61.8 Å
Rg (实空间) rg_real	19.25 Å
Rg 误差 (实空间) rg_real_error	0.33 Å
I(0) (实空间) i0_real	2.4530e+07
I(0) 误差 (实空间) i0_real_error	3.0160e+05
Rg (倒空间) rg_reciprocal	19.26 Å
I(0) (倒空间) i0_reciprocal	24530000.0000
解质量估计 total_estimate	0.9008
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	60.9 Å
偏度 Skewness skewness	0.234
峰度 Kurtosis kurtosis	-0.472
角度范围 angular_range	— – 0.4100 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	4564000.0000
实空间数据点数 n_real_points	72
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.904; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.996

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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	Albicidin resistance protein
分子量 formula_weight	26081.4 kDa
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	2079

GMYDRWFSQQELQVLPFAEQDEQRNQTWLELVGEAQQLMGERCPADEPRAIALATRWMEQLEQDTAGRPEFLTRLNEMHAAEPQMREQTGVTPEMIDFITRAFAESKLAIWARYLNAEELAFTRQHYFDRLMEWPALVADLHRACREKRDPASPEGQQLAQRWLALFQSYAGKDAQTQQKFRYAMEQEPHLMKGTWMTSEVLSWLQQAIGVMMRQAQGPAAEGS

来源 Source

来源生物 organism	Klebsiella oxytoca
NCBI 分类编号 ncbi_taxonomy_id	571
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	;4-[4-[4-[[(6S,6aS)-2-methoxy-6-oxidanyl-11-oxidanylidene-5,6,6a,7,8,9-hexahydropyrrolo[2,1-c][1,4]benzodiazepin-3-yl]oxy]butanoylamino]phenyl]-1-methyl-N-[4-(2-morpholin-4-ylethoxy)phenyl]pyrrole-2-carboxamide ;
分子量 formula_weight	752.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 3 non-polymer

描述 description	;4-[4-[4-[[(6R,6aS)-2-methoxy-6-oxidanyl-11-oxidanylidene-5,6,6a,7,8,9-hexahydropyrrolo[2,1-c][1,4]benzodiazepin-3-yl]oxy]butanoylamino]phenyl]-1-methyl-N-[4-(2-morpholin-4-ylethoxy)phenyl]pyrrole-2-carboxamide ;
分子量 formula_weight	752.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 4 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	3

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	85

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7. 引用文献 (1)

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晶胞边长 a length_a	80.893 Å
晶胞边长 b length_b	80.893 Å
晶胞边长 c length_c	64.863 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.00 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

空间群 space_group	P 43 21 2
空间群编号 int_tables_number	96
晶系 crystal_system	—

分辨率 resolution	1.740 Å
最低分辨率 resolution_low	57.200 Å
R 因子 r_factor	0.2060
R_work r_work	0.2047
R_free r_free	0.2297

fit	/app/data/saxs_computation/i4/9i4j/9i4j.fit
pddf	/app/data/pr_computation/i4/9i4j/9i4j.pr.out
profile	/app/data/saxs_computation/i4/9i4j/9i4j.dat

X-ray structure of the drug binding domain of AlbA in complex with the KMR-04-161 compound of the pyrrolobenzodiazepines class

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