9i9r

X-ray structure of the drug binding domain of AlbA in complex with the KMR-04-163 compound of the pyrrolobenzodiazepines class

Method: X-RAY DIFFRACTION D_max: 104.4 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	9i9r
沉积日期 deposition_date	2025-02-06
最后修订 last_revision	2026-02-18
结构标题 title	X-ray structure of the drug binding domain of AlbA in complex with the KMR-04-163 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	31.72 Å
回转半径 Rg (电子) rg_electron	31.40 Å
零角强度 I(0) i0	197964000.00
分子量 molecular_weight	74710.0 kDa
排除体积 excluded_volume	71985 Å³
包络体积 envelope_volume	127910 Å³
水化壳体积 shell_volume	35510 Å³
包络直径 envelope_diameter	109.8 Å
壳层 Rg shell_rg	37.00 Å
包络 Rg envelope_rg	31.26 Å
形状 Rg shape_rg	31.37 Å
总 Rg total_rg	31.78 Å
总原子数 total_atoms	5637
残基数 n_residues	648
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	104.4 Å
Rg (实空间) rg_real	31.91 Å
Rg 误差 (实空间) rg_real_error	0.93 Å
I(0) (实空间) i0_real	1.9800e+08
I(0) 误差 (实空间) i0_real_error	3.3300e+06
Rg (倒空间) rg_reciprocal	31.83 Å
I(0) (倒空间) i0_reciprocal	198000000.0000
解质量估计 total_estimate	0.8606
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	33.4 Å
偏度 Skewness skewness	0.498
峰度 Kurtosis kurtosis	-0.294
角度范围 angular_range	— – 0.2500 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	17680000.0000
实空间数据点数 n_real_points	51
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.844; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.960; Smooth: 0.692

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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	Albicidin resistance protein
分子量 formula_weight	26081.4 kDa
来源方法 src_method	man
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	C,A,B
原子数 atom_count	5835

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-[[(6~{S},6~{a}~{S})-2-methoxy-6-oxidanyl-11-oxidanylidene-5,6,6~{a},7,8,9-hexahydropyrrolo[2,1-c][1,4]benzodiazepin-3-yl]oxy]butanoylamino]phenyl]-~{N}-(1-benzothiophen-5-yl)-1-methyl-pyrrole-2-carboxamide ;
分子量 formula_weight	679.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 3 non-polymer

描述 description	;4-[4-[4-[[(6~{a}~{S})-2-methoxy-11-oxidanylidene-6~{a},7,8,9-tetrahydropyrrolo[2,1-c][1,4]benzodiazepin-3-yl]oxy]butanoylamino]phenyl]-~{N}-(1-benzothiophen-5-yl)-1-methyl-pyrrole-2-carboxamide ;
分子量 formula_weight	661.8 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	24

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7. 引用文献 (1)

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晶胞边长 a length_a	184.703 Å
晶胞边长 b length_b	120.180 Å
晶胞边长 c length_c	54.696 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	91.51 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	12

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	monoclinic

分辨率 resolution	2.580 Å
最低分辨率 resolution_low	100.720 Å
R 因子 r_factor	0.1968
R_work r_work	0.1952
R_free r_free	0.2271

fit	/app/data/saxs_computation/i9/9i9r/9i9r.fit
pddf	/app/data/pr_computation/i9/9i9r/9i9r.pr.out
profile	/app/data/saxs_computation/i9/9i9r/9i9r.dat

X-ray structure of the drug binding domain of AlbA in complex with the KMR-04-163 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