8sbu

Crystal structure of MBP fusion with HPPK from Methanocaldococcus jannaschii

Method: X-RAY DIFFRACTION D_max: 107.0 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	8sbu
沉积日期 deposition_date	2023-04-04
最后修订 last_revision	2024-07-03
结构标题 title	Crystal structure of MBP fusion with HPPK from Methanocaldococcus jannaschii
关键词 keywords	MBP fusion, HPPK, Methanocaldococcus jannaschii, TRANSFERASE; TRANSFERASE
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	33.68 Å
回转半径 Rg (电子) rg_electron	32.91 Å
零角强度 I(0) i0	237708000.00
分子量 molecular_weight	129640.0 kDa
排除体积 excluded_volume	164610 Å³
包络体积 envelope_volume	200770 Å³
水化壳体积 shell_volume	49857 Å³
包络直径 envelope_diameter	114.7 Å
壳层 Rg shell_rg	40.53 Å
包络 Rg envelope_rg	32.79 Å
形状 Rg shape_rg	32.86 Å
总 Rg total_rg	33.69 Å
总原子数 total_atoms	9153
残基数 n_residues	1168
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	107.0 Å
Rg (实空间) rg_real	33.57 Å
Rg 误差 (实空间) rg_real_error	0.80 Å
I(0) (实空间) i0_real	2.3770e+08
I(0) 误差 (实空间) i0_real_error	4.1380e+06
Rg (倒空间) rg_reciprocal	33.64 Å
I(0) (倒空间) i0_reciprocal	237700000.0000
解质量估计 total_estimate	0.8864
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	45.5 Å
偏度 Skewness skewness	0.240
峰度 Kurtosis kurtosis	-0.278
角度范围 angular_range	— – 0.2350 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	110000000.0000
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: 0.883; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.873

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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	Maltose/maltodextrin-binding periplasmic protein,6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase
分子量 formula_weight	68721.6 kDa
EC 编号 ec_number	2.7.6.3
突变 mutation	D89A,K90A,E179A,N180A,K246A,E366A,K369A,D370A,R374N,I375A,T376A,K377A,I376A
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	9492

MKIHHHHHHEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPAAAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYAAGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSAVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDAALAAAQTNAAAMDMKEWEIFYNKIMEDFGFDKDKDVESAVILNNILENANTIPVDKLKDIIEGREVFIFGAGPSIKKHINILKELREINYKNPIIVADGACKAFLEENIIPDIIVSDLDGDLEALFECNRKGSIIVVHAHGDNIEKIKKYVPKLKNVVGSCQIPNYKELNLRNVINFGGFTDGDRCCFLAYHFKAKKLILGGMDFGIYITKYSRPNIKEDIAIGDEIKIKKLEYAKTLINYLKDKIEIEFLK

来源 Source

来源生物 organism	Methanocaldococcus jannaschii DSM 2661
NCBI 分类编号 ncbi_taxonomy_id	243232
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 branched

描述 description	alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
分子量 formula_weight	342.3 kDa
来源方法 src_method	man
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	339

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7. 引用文献 (1)

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晶胞边长 a length_a	58.170 Å
晶胞边长 b length_b	69.827 Å
晶胞边长 c length_c	73.121 Å
晶胞夹角 α angle_alpha	67.44 °
晶胞夹角 β angle_beta	74.63 °
晶胞夹角 γ angle_gamma	78.13 °
晶胞分子数 Z z_pdb	2

空间群 space_group	P 1
空间群编号 int_tables_number	1
晶系 crystal_system	—

分辨率 resolution	2.200 Å
最低分辨率 resolution_low	29.279 Å
R 因子 r_factor	0.2222
R_work r_work	0.2212
R_free r_free	0.2740

fit	/app/data/saxs_computation/sb/8sbu/8sbu.fit
pddf	/app/data/pr_computation/sb/8sbu/8sbu.pr.out
profile	/app/data/saxs_computation/sb/8sbu/8sbu.dat

Crystal structure of MBP fusion with HPPK from Methanocaldococcus jannaschii

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