SAXSdb — 2e6b

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2e6b
沉积日期 deposition_date	2006-12-26
结构标题 title	;Crystal structure of the stationary phase survival protein SurE from Thermus thermophilus HB8 in complex with magnesium and tungstate ;
关键词 keywords	SurE protein, complex with magnesium and tungstate ions, Hydrolase; HYDROLASE
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	29.48 Å
回转半径 Rg (电子) rg_electron	28.81 Å
零角强度 I(0) i0	170850000.00
分子量 molecular_weight	104240.0 kDa
排除体积 excluded_volume	130420 Å³
包络体积 envelope_volume	161150 Å³
水化壳体积 shell_volume	45138 Å³
包络直径 envelope_diameter	93.2 Å
壳层 Rg shell_rg	37.59 Å
包络 Rg envelope_rg	28.24 Å
形状 Rg shape_rg	28.85 Å
总 Rg total_rg	29.47 Å
总原子数 total_atoms	7327
残基数 n_residues	933
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	87.7 Å
Rg (实空间) rg_real	29.31 Å
Rg 误差 (实空间) rg_real_error	0.48 Å
I(0) (实空间) i0_real	1.7090e+08
I(0) 误差 (实空间) i0_real_error	2.4620e+06
Rg (倒空间) rg_reciprocal	29.38 Å
I(0) (倒空间) i0_reciprocal	170900000.0000
解质量估计 total_estimate	0.9071
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	40.6 Å
偏度 Skewness skewness	0.139
峰度 Kurtosis kurtosis	-0.497
角度范围 angular_range	— – 0.2700 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	96890000.0000
实空间数据点数 n_real_points	55
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.951; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.960

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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 (6)

Entity 1 polymer

描述 description	;5'-nucleotidase surE ;
分子量 formula_weight	26625.3 kDa
EC 编号 ec_number	3.1.3.5
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	7414

MRILVTNDDGIYSPGLWALAEAASQFGEVFVAAPDTEQSAAGHAITIAHPVRAYPHPSPLHAPHFPAYRVRGTPADCVALGLHLFGPVDLVLSGVNLGSNLGHEIWHSGTVAAAKQGYLFGLSAAAFSVPLNGEVPDFAGLRPWLLRTLETLLRLERPFLVNVNLPLRPKGFLWTRQSVRAYEGVVIPGEDPMGRPFYWFAPRPLKEAEEGTDRWAVAQGFVSATPLRLDLTDETRLQPTLAHD

来源 Source

来源生物 organism	Thermus thermophilus
NCBI 分类编号 ncbi_taxonomy_id	300852
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 3 non-polymer

描述 description	TUNGSTATE(VI)ION
分子量 formula_weight	247.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 4 non-polymer

描述 description	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	10

Entity 5 non-polymer

描述 description	GLYCEROL
分子量 formula_weight	92.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 6 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	87

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6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d2e6ba_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.106 — SurE-like
超家族 Superfamily superfamily	c.106.1 — SurE-like
家族 Family family	c.106.1.0 — automated matches

结构域编号 domain_id	d2e6bb_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.106 — SurE-like
超家族 Superfamily superfamily	c.106.1 — SurE-like
家族 Family family	c.106.1.0 — automated matches

结构域编号 domain_id	d2e6bc_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.106 — SurE-like
超家族 Superfamily superfamily	c.106.1 — SurE-like
家族 Family family	c.106.1.0 — automated matches

结构域编号 domain_id	d2e6bd_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.106 — SurE-like
超家族 Superfamily superfamily	c.106.1 — SurE-like
家族 Family family	c.106.1.0 — automated matches

CATH v4.4 (4 domains)

结构域编号 domain_id	2e6bA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1210 — Stationary-phase Survival Protein Sure Homolog; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 — Survival protein SurE-like phosphatase/nucleotidase

结构域编号 domain_id	2e6bB00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1210 — Stationary-phase Survival Protein Sure Homolog; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 — Survival protein SurE-like phosphatase/nucleotidase

结构域编号 domain_id	2e6bC00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1210 — Stationary-phase Survival Protein Sure Homolog; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 — Survival protein SurE-like phosphatase/nucleotidase

结构域编号 domain_id	2e6bD00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1210 — Stationary-phase Survival Protein Sure Homolog; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 — Survival protein SurE-like phosphatase/nucleotidase

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7. 引用文献 (1)

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晶胞边长 a length_a	132.018 Å
晶胞边长 b length_b	132.018 Å
晶胞边长 c length_c	130.824 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	120.00 °
晶胞分子数 Z z_pdb	24

空间群 space_group	P 31 2 1
空间群编号 int_tables_number	152
晶系 crystal_system	—

分辨率 resolution	2.500 Å
最低分辨率 resolution_low	46.460 Å
R 因子 r_factor	0.1980
R_work r_work	0.1980
R_free r_free	0.2300

fit	/app/data/saxs_computation/e6/2e6b/2e6b.fit
pddf	/app/data/pr_computation/e6/2e6b/2e6b.pr.out
profile	/app/data/saxs_computation/e6/2e6b/2e6b.dat

;Crystal structure of the stationary phase survival protein SurE from Thermus thermophilus HB8 in complex with magnesium and tungstate ;

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution