8xf4

Structure of the siderophore periplasmic binding protein FtsB from Streptococcus pyogenes with Bisucaberin bound

Method: X-RAY DIFFRACTION D_max: 65.8 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

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8xf4
沉积日期 deposition_date	2023-12-13
结构标题 title	Structure of the siderophore periplasmic binding protein FtsB from Streptococcus pyogenes with Bisucaberin bound
关键词 keywords	;Streptococcus pyogenes, siderophore, hydroxamate, FtsB, ABC transporter, alanine scanning, antibiotic strategy, Bisucaberin, METAL BINDING PROTEIN ;; METAL BINDING 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	20.47 Å
回转半径 Rg (电子) rg_electron	19.52 Å
零角强度 I(0) i0	15747100.00
分子量 molecular_weight	31786.0 kDa
排除体积 excluded_volume	40635 Å³
包络体积 envelope_volume	46068 Å³
水化壳体积 shell_volume	19897 Å³
包络直径 envelope_diameter	68.2 Å
壳层 Rg shell_rg	25.85 Å
包络 Rg envelope_rg	19.83 Å
形状 Rg shape_rg	19.48 Å
总 Rg total_rg	20.61 Å
总原子数 total_atoms	2241
残基数 n_residues	274
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	65.8 Å
Rg (实空间) rg_real	20.44 Å
Rg 误差 (实空间) rg_real_error	0.43 Å
I(0) (实空间) i0_real	1.5750e+07
I(0) 误差 (实空间) i0_real_error	1.9910e+05
Rg (倒空间) rg_reciprocal	20.45 Å
I(0) (倒空间) i0_reciprocal	15750000.0000
解质量估计 total_estimate	0.8049
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	25.4 Å
偏度 Skewness skewness	0.347
峰度 Kurtosis kurtosis	-0.316
角度范围 angular_range	— – 0.3900 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	6177000.0000
实空间数据点数 n_real_points	71
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.821; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.000

▶

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

▶

5. 实体与聚合体信息 (4)

Entity 1 polymer

描述 description	Iron-hydroxamate ABC transporter substrate-binding protein FtsB
分子量 formula_weight	31849.5 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	2330

SNTASKSLSPMPQIAGVTYYGDIPKQPKRVVSLASTYTGYLKKLDMNLVGVTSYDKKNPILAKTVKKAKQVAATDLEAITTLKPDLIVVGSTEENIKQLAEIAPVISIEYRKRDYLQVLSDFGRIFNKEGKAKKWLKDWKTKTAAYEKEVKAVTGDKATFTIMGLYEKDVYLFGKDWGRGGEIIHQAFHYDAPEKVKTEVFKQGYLSLSQEVLPDYIGDYVVIAAEDDKTGSALYESKLWQSIPAVKKHHVIKVNANVFYFTDPLSLEYQLETLREAILSSEN

来源 Source

来源生物 organism	Streptococcus pyogenes SSI-1
NCBI 分类编号 ncbi_taxonomy_id	193567
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

描述 description	1,12-bis(oxidanyl)-1,6,12,17-tetrazacyclodocosane-2,5,13,16-tetrone
分子量 formula_weight	400.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 3 non-polymer

描述 description	FE (III) ION
分子量 formula_weight	55.8 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	89

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	59.974 Å
晶胞边长 b length_b	62.099 Å
晶胞边长 c length_c	67.926 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	2.000 Å
最低分辨率 resolution_low	45.800 Å
R 因子 r_factor	—
R_work r_work	0.1991
R_free r_free	0.2340

fit	/app/data/saxs_computation/xf/8xf4/8xf4.fit
pddf	/app/data/pr_computation/xf/8xf4/8xf4.pr.out
profile	/app/data/saxs_computation/xf/8xf4/8xf4.dat

Structure of the siderophore periplasmic binding protein FtsB from Streptococcus pyogenes with Bisucaberin bound

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