9kgt

;Crystal structure of topoisomerase IV from Klebsiella pneumoniae in complex with DNA and BWC0977, a dual-targeting broad-spectrum novel bacterial topoisomerase inhibitor. ;

Method: X-RAY DIFFRACTION D_max: 197.8 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	9kgt
沉积日期 deposition_date	2024-11-09
结构标题 title	;Crystal structure of topoisomerase IV from Klebsiella pneumoniae in complex with DNA and BWC0977, a dual-targeting broad-spectrum novel bacterial topoisomerase inhibitor. ;
关键词 keywords	DNA-TOPOISOMERASE, GYRASE, PARC PARE ISOMERASE-DNA-ISOMERASE INHIBITOR COMPLEX, NBTIs, ISOMERASE-DNA-ISOMERASE INHIBITOR complex; ISOMERASE/DNA/ISOMERASE INHIBITOR
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	58.35 Å
回转半径 Rg (电子) rg_electron	58.14 Å
零角强度 I(0) i0	3879000000.00
分子量 molecular_weight	331470.0 kDa
排除体积 excluded_volume	312410 Å³
包络体积 envelope_volume	664200 Å³
水化壳体积 shell_volume	96153 Å³
包络直径 envelope_diameter	193.7 Å
壳层 Rg shell_rg	59.11 Å
包络 Rg envelope_rg	56.18 Å
形状 Rg shape_rg	58.04 Å
总 Rg total_rg	58.32 Å
总原子数 total_atoms	24887
残基数 n_residues	2982
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	197.8 Å
Rg (实空间) rg_real	58.53 Å
Rg 误差 (实空间) rg_real_error	2.10 Å
I(0) (实空间) i0_real	3.8790e+09
I(0) 误差 (实空间) i0_real_error	8.0670e+07
Rg (倒空间) rg_reciprocal	58.15 Å
I(0) (倒空间) i0_reciprocal	3877000000.0000
解质量估计 total_estimate	0.8409
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	51.3 Å
偏度 Skewness skewness	0.301
峰度 Kurtosis kurtosis	-0.798
角度范围 angular_range	— – 0.1350 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	170100000.0000
实空间数据点数 n_real_points	28
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.728; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.923; Smooth: 0.819

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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	DNA topoisomerase 4 subunit B,DNA topoisomerase 4 subunit A
分子量 formula_weight	83143.1 kDa
EC 编号 ec_number	5.6.2.2
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	24940

MGSSGKLADCTAQDLNRTELFLVEGDSAGGSAKQARDREYQAIMPLKGKILNTWEVSSDEVLASQEVHDISVAIGIDPDSDDLSQLRYGKICILADADSDGLHIATLLCALFVRHFRTLVKEGHVYVALPPLYRIDLGKEVYYALTEEEKTGVLEQLKRKKGKPNVQRFKGLGEMNPMQLRETTLDPNTRRLVQLVISDEDEQQTTAIMDMLLAKKRSEDRRNWLQEKGDMADLEVESMSDMAERLALHEFTENAYLNYSMYVIMDRALPFIGDGLKPVQRRIVYAMSELGLNASAKFKKSARTVGDVLGKYHPHGDSACYEAMVLMAQPFSYRYPLVDGQGNWGAPDDPKSFAAMRYTESRLSKYAELLLSELGQGTVDWVPNFDGTLQEPKMLPARLPNILLNGTTGIAVGMATDIPPHNLREVAKAAITLIEQPKTTLDELLDIVQGPDFPTEAEIITSRAEIRKIYQNGRGSVRMRAVWSKEDGAVVISALPHQVSGAKVLEQIAAQMRNKKLPMVDDLRDESDHENPTRLVIVPRSNRVDMEQVMNHLFATTDLEKSYRINLNMIGLDGRPAVKNLLEILSEWLVFRRDTVRRRLNHRLEKVLKRLHILEGLLVAFLNIDEVIEIIRTEDEPKPALMSRFGISETQAEAILELKLRHLAKLEEMKIRGEQSELEKERDQLQAILASERKMNNLLKKELQADADAFGDDRRSPLHEREEAKALEHHHHHH

来源 Source

来源生物 organism	Klebsiella pneumoniae subsp. pneumoniae MGH 78578
NCBI 分类编号 ncbi_taxonomy_id	272620
宿主生物 host_organism	Escherichia coli

Entity 2 polymer

描述 description	;DNA (5'-D(PTPTPAPCPGPTPTPGPTPAPTPGPAPTPCPAPTPAPCPAPAPCPGPTPAPA)-3') ;
分子量 formula_weight	7985.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polydeoxyribonucleotide
链编号 strand_id	E,F,G,H

TTACGTTGTATGATCATACAACGTAA

Entity 3 non-polymer

描述 description	;6-[(5S)-5-[[[2-(7-Fluoro-1,2-dihydro-1-methyl-2-oxo-8-quinolinyl)ethyl]amino]methyl]-2-oxo-3-oxazolidinyl]-2H-pyrazino[2,3-b]-1,4-oxazin-3(4H)-one ;
分子量 formula_weight	468.4 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	53

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7. 引用文献 (1)

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晶胞边长 a length_a	95.444 Å
晶胞边长 b length_b	163.265 Å
晶胞边长 c length_c	145.842 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	94.55 °
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	monoclinic

分辨率 resolution	3.050 Å
最低分辨率 resolution_low	46.460 Å
R 因子 r_factor	0.2255
R_work r_work	0.2233
R_free r_free	0.2686

fit	/app/data/saxs_computation/kg/9kgt/9kgt.fit
pddf	/app/data/pr_computation/kg/9kgt/9kgt.pr.out
profile	/app/data/saxs_computation/kg/9kgt/9kgt.dat

;Crystal structure of topoisomerase IV from Klebsiella pneumoniae in complex with DNA and BWC0977, a dual-targeting broad-spectrum novel bacterial topoisomerase inhibitor. ;

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

5. 实体与聚合体信息 (4)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

Entity 3 non-polymer

Entity 4 water

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)