2j4e

THE ITP COMPLEX OF HUMAN INOSINE TRIPHOSPHATASE

Method: X-RAY DIFFRACTION D_max: 141.2 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	2j4e
沉积日期 deposition_date	2006-08-29
结构标题 title	THE ITP COMPLEX OF HUMAN INOSINE TRIPHOSPHATASE
关键词 keywords	;NUCLEOTIDE METABOLISM, ITP, IMP, HYDROLASE, DISEASE MUTATION, INOSINE TRIPHOSPHATE PYROPHOSPHOHYDROLASE, INOSINE TRIPHOSPHATASE DEFICIENCY ;; 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	41.53 Å
回转半径 Rg (电子) rg_electron	41.72 Å
零角强度 I(0) i0	450386000.00
分子量 molecular_weight	172930.0 kDa
排除体积 excluded_volume	216050 Å³
包络体积 envelope_volume	287540 Å³
水化壳体积 shell_volume	59821 Å³
包络直径 envelope_diameter	151.9 Å
壳层 Rg shell_rg	44.62 Å
包络 Rg envelope_rg	42.04 Å
形状 Rg shape_rg	41.71 Å
总 Rg total_rg	41.92 Å
总原子数 total_atoms	12129
残基数 n_residues	1521
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	141.2 Å
Rg (实空间) rg_real	41.67 Å
Rg 误差 (实空间) rg_real_error	1.38 Å
I(0) (实空间) i0_real	4.5040e+08
I(0) 误差 (实空间) i0_real_error	9.0650e+06
Rg (倒空间) rg_reciprocal	41.53 Å
I(0) (倒空间) i0_reciprocal	450300000.0000
解质量估计 total_estimate	0.8679
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	44.6 Å
偏度 Skewness skewness	0.453
峰度 Kurtosis kurtosis	-0.252
角度范围 angular_range	— – 0.1900 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	40290000.0000
实空间数据点数 n_real_points	39
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.845; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.754

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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	INOSINE TRIPHOSPHATE PYROPHOSPHATASE
分子量 formula_weight	21612.8 kDa
EC 编号 ec_number	3.6.1.19
来源方法 src_method	man
拷贝数 entity_count	8

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F,G,H
原子数 atom_count	12296

GSMAASLVGKKIVFVTGNAKKLEEVVQILGDKFPCTLVAQKIDLPEYQGEPDEISIQKCQEAVRQVQGPVLVEDTCLCFNALGGLPGPYIKWFLEKLKPEGLHQLLAGFEDKSAYALCTFALSTGDPSQPVRLFRGRTSGRIVAPRGCQDFGWDPCFQPDGYEQTYAEMPKAEKNAVSHRFRALLELQEYFGSLAA

来源 Source

来源生物 organism	HOMO SAPIENS
通用名 common_name	HUMAN
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 non-polymer

描述 description	;INOSINE 5'-TRIPHOSPHATE ;
分子量 formula_weight	508.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	7

Entity 3 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	8

Entity 4 non-polymer

描述 description	PYROPHOSPHATE 2-
分子量 formula_weight	176.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 non-polymer

描述 description	INOSINIC ACID
分子量 formula_weight	348.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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	167

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6. 折叠分类 (SCOP + CATH) 17 domains

SCOP 2.08 (9 domains)

结构域编号 domain_id	d2j4ea_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.51 — Anticodon-binding domain-like
超家族 Superfamily superfamily	c.51.4 — ITPase-like
家族 Family family	c.51.4.0 — automated matches

结构域编号 domain_id	d2j4eb_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.51 — Anticodon-binding domain-like
超家族 Superfamily superfamily	c.51.4 — ITPase-like
家族 Family family	c.51.4.0 — automated matches

结构域编号 domain_id	d2j4ec_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.51 — Anticodon-binding domain-like
超家族 Superfamily superfamily	c.51.4 — ITPase-like
家族 Family family	c.51.4.0 — automated matches

结构域编号 domain_id	d2j4ed2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.51 — Anticodon-binding domain-like
超家族 Superfamily superfamily	c.51.4 — ITPase-like
家族 Family family	c.51.4.0 — automated matches

结构域编号 domain_id	d2j4ed3
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d2j4ee_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.51 — Anticodon-binding domain-like
超家族 Superfamily superfamily	c.51.4 — ITPase-like
家族 Family family	c.51.4.0 — automated matches

结构域编号 domain_id	d2j4ef_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.51 — Anticodon-binding domain-like
超家族 Superfamily superfamily	c.51.4 — ITPase-like
家族 Family family	c.51.4.0 — automated matches

结构域编号 domain_id	d2j4eg_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.51 — Anticodon-binding domain-like
超家族 Superfamily superfamily	c.51.4 — ITPase-like
家族 Family family	c.51.4.0 — automated matches

结构域编号 domain_id	d2j4eh_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.51 — Anticodon-binding domain-like
超家族 Superfamily superfamily	c.51.4 — ITPase-like
家族 Family family	c.51.4.0 — automated matches

CATH v4.4 (8 domains)

结构域编号 domain_id	2j4eA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	950 — Maf protein
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	2j4eB00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	950 — Maf protein
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	2j4eC00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	950 — Maf protein
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	2j4eD00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	950 — Maf protein
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	2j4eE00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	950 — Maf protein
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	2j4eF00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	950 — Maf protein
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	2j4eG00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	950 — Maf protein
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	2j4eH00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	950 — Maf protein
同源超家族 H-superfamily homologous superfamily	10 —

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7. 引用文献 (1)

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晶胞边长 a length_a	67.998 Å
晶胞边长 b length_b	75.292 Å
晶胞边长 c length_c	110.793 Å
晶胞夹角 α angle_alpha	85.12 °
晶胞夹角 β angle_beta	77.72 °
晶胞夹角 γ angle_gamma	69.19 °
晶胞分子数 Z z_pdb	8

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

分辨率 resolution	2.800 Å
最低分辨率 resolution_low	19.810 Å
R 因子 r_factor	0.2040
R_work r_work	0.2010
R_free r_free	0.2650

fit	/app/data/saxs_computation/j4/2j4e/2j4e.fit
pddf	/app/data/pr_computation/j4/2j4e/2j4e.pr.out
profile	/app/data/saxs_computation/j4/2j4e/2j4e.dat