9ink

Crystal structure of beta-carotene-binding protein (BBP) from Schistocerca gregaria complexed with beta-carotene

Method: X-RAY DIFFRACTION D_max: 136.6 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

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	9ink
沉积日期 deposition_date	2024-07-08
结构标题 title	Crystal structure of beta-carotene-binding protein (BBP) from Schistocerca gregaria complexed with beta-carotene
关键词 keywords	;Complex with beta-carotene, carotenoprotein, takeout-1 domain, tubular lipid-binding protein (TULIPs), carotenoid solubilizer, dimer, LIPID BINDING PROTEIN ;; LIPID BINDING 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	37.79 Å
回转半径 Rg (电子) rg_electron	37.95 Å
零角强度 I(0) i0	30864000.00
分子量 molecular_weight	46303.0 kDa
排除体积 excluded_volume	58940 Å³
包络体积 envelope_volume	76499 Å³
水化壳体积 shell_volume	20551 Å³
包络直径 envelope_diameter	130.9 Å
壳层 Rg shell_rg	35.10 Å
包络 Rg envelope_rg	38.51 Å
形状 Rg shape_rg	37.91 Å
总 Rg total_rg	37.84 Å
总原子数 total_atoms	3269
残基数 n_residues	441
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	136.6 Å
Rg (实空间) rg_real	38.79 Å
Rg 误差 (实空间) rg_real_error	1.98 Å
I(0) (实空间) i0_real	3.0860e+07
I(0) 误差 (实空间) i0_real_error	5.4740e+05
Rg (倒空间) rg_reciprocal	38.17 Å
I(0) (倒空间) i0_reciprocal	30840000.0000
解质量估计 total_estimate	0.5659
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	22.8 Å
偏度 Skewness skewness	0.618
峰度 Kurtosis kurtosis	-0.595
角度范围 angular_range	— – 0.2100 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	4757000.0000
实空间数据点数 n_real_points	43
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.105; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.040; Smooth: 0.000

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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	Yellow protein of the takeout family
分子量 formula_weight	26239.8 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	3274

GPHMGVQTCNASSPDFQLCVRASLQQLIPELASGVPSIGAEGVDPLRGLPPIVHNSNGFKVQLDDVSISGLSATLINDVNVDLTSNTIRIQATVPGYITATGIQTTDAEIMGIPLKGSGPFTISLANPSLAVTLTGAPSAGPNGQTYLRLTSASAAIEPGTPTADIKGFFPQFPPLEAAASAFASVVAPDVVQSLKPTLDKWLGGVALQRAQAVFSSVSYDALFPGRTPAAVGLYRAVPGLHTLPLPLSAFAYHK

来源 Source

来源生物 organism	Schistocerca gregaria
NCBI 分类编号 ncbi_taxonomy_id	7010
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

描述 description	BETA-CAROTENE
分子量 formula_weight	536.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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	5

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7. 引用文献 (1)

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晶胞边长 a length_a	55.390 Å
晶胞边长 b length_b	75.510 Å
晶胞边长 c length_c	224.220 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	16

空间群 space_group	C 2 2 21
空间群编号 int_tables_number	20
晶系 crystal_system	—

分辨率 resolution	2.700 Å
最低分辨率 resolution_low	28.880 Å
R 因子 r_factor	0.2241
R_work r_work	0.2212
R_free r_free	0.2777

fit	/app/data/saxs_computation/in/9ink/9ink.fit
pddf	/app/data/pr_computation/in/9ink/9ink.pr.out
profile	/app/data/saxs_computation/in/9ink/9ink.dat

Crystal structure of beta-carotene-binding protein (BBP) from Schistocerca gregaria complexed with beta-carotene

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