1fpd

;STRUCTURAL ASPECTS OF THE ALLOSTERIC INHIBITION OF FRUCTOSE-1,6-BISPHOSPHATASE BY AMP: THE BINDING OF BOTH THE SUBSTRATE ANALOGUE 2,5-ANHYDRO-D-GLUCITOL-1,6-BISPHOSPHATE AND CATALYTIC METAL IONS MONITORED BY X-RAY CRYSTALLOGRAPHY ;

Method: X-RAY DIFFRACTION D_max: 88.1 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	1fpd
沉积日期 deposition_date	1994-12-15
结构标题 title	;STRUCTURAL ASPECTS OF THE ALLOSTERIC INHIBITION OF FRUCTOSE-1,6-BISPHOSPHATASE BY AMP: THE BINDING OF BOTH THE SUBSTRATE ANALOGUE 2,5-ANHYDRO-D-GLUCITOL-1,6-BISPHOSPHATE AND CATALYTIC METAL IONS MONITORED BY X-RAY CRYSTALLOGRAPHY ;
关键词 keywords	HYDROLASE (PHOSPHORIC MONOESTER); HYDROLASE (PHOSPHORIC MONOESTER)
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	26.66 Å
回转半径 Rg (电子) rg_electron	25.60 Å
零角强度 I(0) i0	80030000.00
分子量 molecular_weight	70731.0 kDa
排除体积 excluded_volume	88846 Å³
包络体积 envelope_volume	103370 Å³
水化壳体积 shell_volume	33015 Å³
包络直径 envelope_diameter	91.7 Å
壳层 Rg shell_rg	33.51 Å
包络 Rg envelope_rg	25.87 Å
形状 Rg shape_rg	25.62 Å
总 Rg total_rg	26.35 Å
总原子数 total_atoms	6032
残基数 n_residues	634
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	88.1 Å
Rg (实空间) rg_real	26.60 Å
Rg 误差 (实空间) rg_real_error	0.62 Å
I(0) (实空间) i0_real	8.0030e+07
I(0) 误差 (实空间) i0_real_error	1.1660e+06
Rg (倒空间) rg_reciprocal	26.62 Å
I(0) (倒空间) i0_reciprocal	80030000.0000
解质量估计 total_estimate	0.8888
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	29.4 Å
偏度 Skewness skewness	0.296
峰度 Kurtosis kurtosis	-0.411
角度范围 angular_range	— – 0.3000 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	21870000.0000
实空间数据点数 n_real_points	61
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.857; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.983

▶

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

▶

5. 实体与聚合体信息 (5)

Entity 1 polymer

描述 description	FRUCTOSE 1,6-BISPHOSPHATASE
分子量 formula_weight	36503.0 kDa
EC 编号 ec_number	3.1.3.11
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	6470

TDQAAFDTNIVTLTRFVMEQGRKARGTGEMTQLLNSLCTAVKAISTAVRKAGIAHLYGIAGSTNVTGDQVKKLDVLSNDLVINVLKSSFATCVLVTEEDKNAIIVEPEKRGKYVVCFDPLDGSSNIDCLVSIGTIFGIYRKNSTDEPSEKDALQPGRNLVAAGYALYGSATMLVLAMVNGVNCFMLDPAIGEFILVDRNVKIKKKGSIYSINEGYAKEFDPAITEYIQRKKFPPDNSAPYGARYVGSMVADVHRTLVYGGIFMYPANKKSPKGKLRLLYECNPMAYVMEKAGGLATTGKEAVLDIVPTDIHQRAPIILGSPEDVTELLEIYQKHA

来源 Source

来源生物 organism	Sus scrofa
通用名 common_name	pig
NCBI 分类编号 ncbi_taxonomy_id	9823

Entity 2 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	4

Entity 3 non-polymer

描述 description	2,5-anhydro-1,6-di-O-phosphono-D-glucitol
分子量 formula_weight	324.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 non-polymer

描述 description	ADENOSINE MONOPHOSPHATE
分子量 formula_weight	347.2 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	146

▼

6. 折叠分类 (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d1fpda_
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	d1fpdb_
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	1fpdA01
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	1fpdA02
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	1fpdB01
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	1fpdB02
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 —

▶

7. 引用文献 (4)

▶

晶胞边长 a length_a	61.100 Å
晶胞边长 b length_b	166.400 Å
晶胞边长 c length_c	79.900 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	8

空间群 space_group	P 21 21 2
空间群编号 int_tables_number	18
晶系 crystal_system	—

分辨率 resolution	2.100 Å
最低分辨率 resolution_low	8.000 Å
R 因子 r_factor	0.1910
R_work r_work	0.1910
R_free r_free	—

fit	/app/data/saxs_computation/fp/1fpd/1fpd.fit
pddf	/app/data/pr_computation/fp/1fpd/1fpd.pr.out
profile	/app/data/saxs_computation/fp/1fpd/1fpd.dat