9f8m

;Crystal Structure of PhzA/B from Burkholderia cepacia R18194 in complex with [6-Hydroxy-2-(4-hydroxyphenyl)benzo[b]thiophen-3-yl][4-(propylamino)phenyl]methanone ;

Method: X-RAY DIFFRACTION D_max: 114.0 Å Quality: REASONABLE

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

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	9f8m
沉积日期 deposition_date	2024-05-06
最后修订 last_revision	2025-04-16
结构标题 title	;Crystal Structure of PhzA/B from Burkholderia cepacia R18194 in complex with [6-Hydroxy-2-(4-hydroxyphenyl)benzo[b]thiophen-3-yl][4-(propylamino)phenyl]methanone ;
关键词 keywords	;pyocyanin, phenazine biosynthesis, virulence, inhibitor, ketosteroid-isomerase, cocrystal, PhzA/B, Burkholderia cepacia, BIOSYNTHETIC PROTEIN ;; BIOSYNTHETIC PROTEIN
实验方法 method	X-RAY DIFFRACTION

▼

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	33.54 Å
回转半径 Rg (电子) rg_electron	33.49 Å
零角强度 I(0) i0	84966700.00
分子量 molecular_weight	72603.0 kDa
排除体积 excluded_volume	90106 Å³
包络体积 envelope_volume	111410 Å³
水化壳体积 shell_volume	29524 Å³
包络直径 envelope_diameter	113.6 Å
壳层 Rg shell_rg	37.41 Å
包络 Rg envelope_rg	33.53 Å
形状 Rg shape_rg	33.50 Å
总 Rg total_rg	33.74 Å
总原子数 total_atoms	9944
残基数 n_residues	616
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

▼

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	114.0 Å
Rg (实空间) rg_real	33.82 Å
Rg 误差 (实空间) rg_real_error	0.99 Å
I(0) (实空间) i0_real	8.4970e+07
I(0) 误差 (实空间) i0_real_error	1.6290e+06
Rg (倒空间) rg_reciprocal	33.65 Å
I(0) (倒空间) i0_reciprocal	84950000.0000
解质量估计 total_estimate	0.5772
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	26.7 Å
偏度 Skewness skewness	0.487
峰度 Kurtosis kurtosis	-0.584
角度范围 angular_range	— – 0.2350 Å⁻¹
当前正则化参数 α current_alpha	0.0002
最高正则化参数 α highest_alpha	18640000.0000
实空间数据点数 n_real_points	48
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.666; Stabil: 1.000; Sysdev: 0.078; Positv: 1.000; Valcen: 0.495; Smooth: 0.770

▶

4. 晶体学与实验 4. Crystallography & Experiment

▶

5. 实体与聚合体信息 (5)

Entity 1 polymer

描述 description	Phenazine biosynthesis protein A/B
分子量 formula_weight	21531.0 kDa
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	10677

MGSSHHHHHHSSGLVPRGSHMSDVESLENTSENRAQVAARQHNRKIVEQYMHTRGEARLKRHLLFTEDGVGGLWTTDSGQPIAIRGREKLGEHAVWSLQCFPDWVWTDIQIFETQDPNWFWVECRGEGAIVFPGYPRGQYRNHFLHSFRFENGLIKEQREFMNPCEQFRSLGIEVPEVRRDGLPS

来源 Source

来源生物 organism	Burkholderia lata
NCBI 分类编号 ncbi_taxonomy_id	482957
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

描述 description	GLYCEROL
分子量 formula_weight	92.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	5

Entity 3 non-polymer

描述 description	[2-(4-hydroxyphenyl)-6-oxidanyl-1-benzothiophen-3-yl]-[4-(propylamino)phenyl]methanone
分子量 formula_weight	403.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

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	1

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	595

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	69.251 Å
晶胞边长 b length_b	68.392 Å
晶胞边长 c length_c	83.838 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.20 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

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	1.430 Å
最低分辨率 resolution_low	48.660 Å
R 因子 r_factor	0.1586
R_work r_work	0.1571
R_free r_free	0.1867

fit	/app/data/saxs_computation/f8/9f8m/9f8m.fit
pddf	/app/data/pr_computation/f8/9f8m/9f8m.pr.out
profile	/app/data/saxs_computation/f8/9f8m/9f8m.dat

;Crystal Structure of PhzA/B from Burkholderia cepacia R18194 in complex with [6-Hydroxy-2-(4-hydroxyphenyl)benzo[b]thiophen-3-yl][4-(propylamino)phenyl]methanone ;

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