1lby

;Crystal Structure of a complex (P32 crystal form) of dual activity FBPase/IMPase (AF2372) from Archaeoglobus fulgidus with 3 Manganese ions, Fructose-6-Phosphate, and Phosphate ion ;

Method: X-RAY DIFFRACTION D_max: 78.7 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	1lby
沉积日期 deposition_date	2002-04-04
结构标题 title	;Crystal Structure of a complex (P32 crystal form) of dual activity FBPase/IMPase (AF2372) from Archaeoglobus fulgidus with 3 Manganese ions, Fructose-6-Phosphate, and Phosphate ion ;
关键词 keywords	dual activity, FBPase, IMPase, archaeal phosphatase, product complex, 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	23.83 Å
回转半径 Rg (电子) rg_electron	22.95 Å
零角强度 I(0) i0	55335200.00
分子量 molecular_weight	56957.0 kDa
排除体积 excluded_volume	70795 Å³
包络体积 envelope_volume	79231 Å³
水化壳体积 shell_volume	28236 Å³
包络直径 envelope_diameter	82.8 Å
壳层 Rg shell_rg	30.54 Å
包络 Rg envelope_rg	23.22 Å
形状 Rg shape_rg	22.95 Å
总 Rg total_rg	23.77 Å
总原子数 total_atoms	3980
残基数 n_residues	504
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	78.7 Å
Rg (实空间) rg_real	23.78 Å
Rg 误差 (实空间) rg_real_error	0.49 Å
I(0) (实空间) i0_real	5.5340e+07
I(0) 误差 (实空间) i0_real_error	6.9480e+05
Rg (倒空间) rg_reciprocal	23.80 Å
I(0) (倒空间) i0_reciprocal	55340000.0000
解质量估计 total_estimate	0.8045
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	28.3 Å
偏度 Skewness skewness	0.338
峰度 Kurtosis kurtosis	-0.258
角度范围 angular_range	— – 0.3350 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	16860000.0000
实空间数据点数 n_real_points	65
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.820; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; 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 (5)

Entity 1 polymer

描述 description	fructose 1,6-bisphosphatase/inositol monophosphatase
分子量 formula_weight	28002.8 kDa
EC 编号 ec_number	3.1.3.11, 3.1.3.25
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	4166

MDERDALRISREIAGEVRKAIASMPLRERVKDVGMGKDGTPTKAADRVAEDAALEILRKERVTVVTEESGVLGEGDVFVALDPLDGTFNATRGIPVYSVSLCFSYSDKLKDAFFGYVYNLATGDEYYADSSGAYRNGERIEVSDAEELYCNAIIYYPDRKFPFKRMRIFGSAATELCFFADGSFDCFLDIRPGKMLRIYDAAAGVFIAEKAGGKVTELDGESLGNKKFDMQERLNIVAANEKLHPKLLELIK

来源 Source

来源生物 organism	Archaeoglobus fulgidus
NCBI 分类编号 ncbi_taxonomy_id	2234
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	6-O-phosphono-beta-D-fructofuranose
分子量 formula_weight	260.1 kDa
来源方法 src_method	man
拷贝数 entity_count	2

Entity 3 non-polymer

描述 description	MANGANESE (II) ION
分子量 formula_weight	54.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

Entity 4 non-polymer

描述 description	PHOSPHATE ION
分子量 formula_weight	95.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 5 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	186

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6. 折叠分类 (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d1lbya_
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.7 — Carbohydrate phosphatase
超家族 Superfamily superfamily	e.7.1 — Carbohydrate phosphatase
家族 Family family	e.7.1.1 — Inositol monophosphatase/fructose-1,6-bisphosphatase-like

结构域编号 domain_id	d1lbyb_
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.7 — Carbohydrate phosphatase
超家族 Superfamily superfamily	e.7.1 — Carbohydrate phosphatase
家族 Family family	e.7.1.1 — Inositol monophosphatase/fructose-1,6-bisphosphatase-like

CATH v4.4 (4 domains)

结构域编号 domain_id	1lbyA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	540 — Fructose-1,6-Bisphosphatase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Fructose-1,6-Bisphosphatase, subunit A, domain 1

结构域编号 domain_id	1lbyA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
同源超家族 H-superfamily homologous superfamily	80 —

结构域编号 domain_id	1lbyB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	540 — Fructose-1,6-Bisphosphatase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Fructose-1,6-Bisphosphatase, subunit A, domain 1

结构域编号 domain_id	1lbyB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
同源超家族 H-superfamily homologous superfamily	80 —

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7. 引用文献 (2)

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晶胞边长 a length_a	89.250 Å
晶胞边长 b length_b	89.250 Å
晶胞边长 c length_c	102.970 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	6

空间群 space_group	P 32
空间群编号 int_tables_number	145
晶系 crystal_system	—

分辨率 resolution	2.250 Å
最低分辨率 resolution_low	30.000 Å
R 因子 r_factor	0.1540
R_work r_work	0.1520
R_free r_free	0.2100

fit	/app/data/saxs_computation/lb/1lby/1lby.fit
pddf	/app/data/pr_computation/lb/1lby/1lby.pr.out
profile	/app/data/saxs_computation/lb/1lby/1lby.dat