9md0

;Crystal structure of the transpeptidase domain of PBP2 from the Neisseria gonorrhoeae cephalosporin decreased susceptibility strain 35/02 in complex with boronate inhibitor VNRX-6752 ;

Method: X-RAY DIFFRACTION D_max: 60.3 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	9md0
沉积日期 deposition_date	2024-12-05
结构标题 title	;Crystal structure of the transpeptidase domain of PBP2 from the Neisseria gonorrhoeae cephalosporin decreased susceptibility strain 35/02 in complex with boronate inhibitor VNRX-6752 ;
关键词 keywords	Neisseria gonorrhoeae cephalosporin resistance Penicillin-binding protein 2 Boronate inhibitor, LIGASE; LIGASE
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	19.44 Å
回转半径 Rg (电子) rg_electron	18.49 Å
零角强度 I(0) i0	40124800.00
分子量 molecular_weight	32817.0 kDa
排除体积 excluded_volume	31720 Å³
包络体积 envelope_volume	50650 Å³
水化壳体积 shell_volume	22006 Å³
包络直径 envelope_diameter	59.9 Å
壳层 Rg shell_rg	25.70 Å
包络 Rg envelope_rg	18.85 Å
形状 Rg shape_rg	18.49 Å
总 Rg total_rg	19.20 Å
总原子数 total_atoms	2490
残基数 n_residues	324
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	60.3 Å
Rg (实空间) rg_real	19.28 Å
Rg 误差 (实空间) rg_real_error	0.25 Å
I(0) (实空间) i0_real	4.0120e+07
I(0) 误差 (实空间) i0_real_error	4.6920e+05
Rg (倒空间) rg_reciprocal	19.30 Å
I(0) (倒空间) i0_reciprocal	40130000.0000
解质量估计 total_estimate	0.8954
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	25.5 Å
偏度 Skewness skewness	0.120
峰度 Kurtosis kurtosis	-0.428
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	10780000.0000
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: 0.884; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.999

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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	Penicillin-binding protein 2
分子量 formula_weight	35331.4 kDa
EC 编号 ec_number	3.4.16.4
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	2525

GSGGALSLDQRIQTLAYEELNKAVEYHQAKAGTVVVLDARTGEILALVNTPGRNRAVTDMIEPGSAMKPFTIAKALDSGKVDATDTFNTLPYKIGSATVQDTHVYPTLDVRGIMQKSSNVGTSKLSAMFTPKEMYDFYHDLGVGVRMHSGFPGETAGLLRSWRRWQKIEQATMSFGYGLQLSLLQLARAYTVLTHDGELLPVSFEKQAVAPKGKRVIKASTAKKVRELMVSVTEAGGTGTAGAVDGFDVGAKTGTARKLVNGRYVDYKHVATFIGFAPAKNPRVIVAVTIDEPTANGYYSGVVTGPVFKQVMGGSLNILGVSPTKPLTNV

来源 Source

来源生物 organism	Neisseria gonorrhoeae 35/02
NCBI 分类编号 ncbi_taxonomy_id	528346
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

描述 description	;(3R)-3-({(2R)-2-(4-carboxyphenyl)-2-[(4-ethyl-2,3-dioxopiperazine-1-carbonyl)amino]acetyl}amino)-2-hydroxy-3,4-dihydro-2H-1,2-benzoxaborinine-8-carboxylic acid ;
分子量 formula_weight	552.3 kDa
来源方法 src_method	nat
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	19

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7. 引用文献 (2)

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晶胞边长 a length_a	50.464 Å
晶胞边长 b length_b	60.224 Å
晶胞边长 c length_c	110.340 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	4

空间群 space_group	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	2.613 Å
最低分辨率 resolution_low	38.680 Å
R 因子 r_factor	—
R_work r_work	0.1749
R_free r_free	0.2319

fit	/app/data/saxs_computation/md/9md0/9md0.fit
pddf	/app/data/pr_computation/md/9md0/9md0.pr.out
profile	/app/data/saxs_computation/md/9md0/9md0.dat

;Crystal structure of the transpeptidase domain of PBP2 from the Neisseria gonorrhoeae cephalosporin decreased susceptibility strain 35/02 in complex with boronate inhibitor VNRX-6752 ;

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