SAXSdb — 8g8f

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8g8f
沉积日期 deposition_date	2023-02-17
结构标题 title	Human IMPDH2 mutant - L245P, treated with ATP, IMP, and NAD+; extended filament segment reconstruction
关键词 keywords	Filament, Dehydrogenase, CBS domain, Bateman domain, purine biosynthesis, OXIDOREDUCTASE; OXIDOREDUCTASE
实验方法 method	ELECTRON MICROSCOPY

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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	52.96 Å
回转半径 Rg (电子) rg_electron	52.39 Å
零角强度 I(0) i0	2934450000.00
分子量 molecular_weight	442150.0 kDa
排除体积 excluded_volume	548850 Å³
包络体积 envelope_volume	841110 Å³
水化壳体积 shell_volume	126660 Å³
包络直径 envelope_diameter	154.4 Å
壳层 Rg shell_rg	63.53 Å
包络 Rg envelope_rg	49.57 Å
形状 Rg shape_rg	52.39 Å
总 Rg total_rg	52.68 Å
总原子数 total_atoms	30912
残基数 n_residues	3928
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	150.7 Å
Rg (实空间) rg_real	52.54 Å
Rg 误差 (实空间) rg_real_error	0.97 Å
I(0) (实空间) i0_real	2.9340e+09
I(0) 误差 (实空间) i0_real_error	5.1960e+07
Rg (倒空间) rg_reciprocal	53.30 Å
I(0) (倒空间) i0_reciprocal	2938000000.0000
解质量估计 total_estimate	0.8651
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	80.4 Å
偏度 Skewness skewness	-0.183
峰度 Kurtosis kurtosis	-0.560
角度范围 angular_range	— – 0.1500 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	152100000.0000
实空间数据点数 n_real_points	31
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.894; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.582

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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 (4)

Entity 1 polymer

描述 description	;Inosine-5'-monophosphate dehydrogenase 2 ;
分子量 formula_weight	56464.5 kDa
EC 编号 ec_number	1.1.1.205
突变 mutation	L245P
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	30912

SEFELMADYLISGGTSYVPDDGLTAQQLFNCGDGLTYNDFLILPGYIDFTADQVDLTSALTKKITLKTPLVSSPMDTVTEAGMAIAMALTGGIGFIHHNCTPEFQANEVRKVKKYEQGFITDPVVLSPKDRVRDVFEAKARHGFCGIPITDTGRMGSRLVGIISSRDIDFLKEEEHDCFLEEIMTKREDLVVAPAGITLKEANEILQRSKKGKLPIVNEDDELVAIIARTDLKKNRDYPLASKDAKKQLPCGAAIGTHEDDKYRLDLLAQAGVDVVVLDSSQGNSIFQINMIKYIKDKYPNLQVIGGNVVTAAQAKNLIDAGVDALRVGMGSGSICITQEVLACGRPQATAVYKVSEYARRFGVPVIADGGIQNVGHIAKALALGASTVMMGSLLAATTEAPGEYFFSDGIRLKKYRGMGSLDAMDKHLSSQNRYFSEADKIKVAQGVSGAVQDKGSIHKFVPYLIAGIQHSCQDIGAKSLTQVRAMMYSGELKFEKRTSSAQVEGGVHSLHSYEKRLF

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	ADENOSINE-5'-TRIPHOSPHATE
分子量 formula_weight	507.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	16

Entity 3 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	8

Entity 4 non-polymer

描述 description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
分子量 formula_weight	663.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	8

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7. 引用文献 (13)

Neurodevelopmental disorder mutations in the purine biosynthetic enzyme IMPDH2 disrupt its allosteric regulation.

J.Biol.Chem. (2023)

PMID: 37414152 · DOI: 10.1016/j.jbc.2023.105012 PRIMARY

Point mutations in IMPDH2 which cause early-onset neurodevelopmental disorders disrupt enzyme regulation and filament structure.

Biorxiv (2023)

PMID: 36993700 · DOI: 10.1101/2023.03.15.532669

Improvement of cryo-EM maps by density modification.

Nat Methods (2020)

PMID: 32807957 · DOI: 10.1038/s41592-020-0914-9

Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.

Acta Crystallogr D Struct Biol (2019)

PMID: 31588918 · DOI: 10.1107/S2059798319011471

ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps.

Acta Crystallogr D Struct Biol (2018)

PMID: 29872003 · DOI: 10.1107/S2059798318002425

New tools for automated high-resolution cryo-EM structure determination in RELION-3.

Elife (2018)

PMID: 30412051 · DOI: 10.1101/384537

Real-space refinement in PHENIX for cryo-EM and crystallography.

Acta Crystallogr D Struct Biol (2018)

PMID: 29872004 · DOI: 10.1107/S2059798318006551

MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy.

Nat Methods (2017)

PMID: 28250466 · DOI: 10.7554/eLife.06980

CTFFIND4: Fast and accurate defocus estimation from electron micrographs.

J Struct Biol (2015)

PMID: 26278980 · DOI: 10.1016/j.jsb.2012.12.006

RELION: implementation of a Bayesian approach to cryo-EM structure determination.

J Struct Biol (2012)

PMID: 23000701 · DOI: 10.1016/j.jsb.2012.05.005

Coot: model-building tools for molecular graphics.

Acta Crystallogr D Biol Crystallogr (2004)

PMID: 15572765 · DOI: 10.1107/S0907444904019158

UCSF Chimera--a visualization system for exploratory research and analysis.

J Comput Chem (2004)

PMID: 15264254 · DOI: 10.1002/jcc.20084

Leginon: an automated system for acquisition of images from vitreous ice specimens.

J Struct Biol (2000)

PMID: 11121305 · DOI: 10.1006/jsbi.2000.4314

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晶胞边长 a length_a	1.000 Å
晶胞边长 b length_b	1.000 Å
晶胞边长 c length_c	1.000 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	—

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

分辨率 resolution	2.60 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	54304

fit	/app/data/saxs_computation/g8/8g8f/8g8f.fit
pddf	/app/data/pr_computation/g8/8g8f/8g8f.pr.out
profile	/app/data/saxs_computation/g8/8g8f/8g8f.dat

Human IMPDH2 mutant - L245P, treated with ATP, IMP, and NAD+; extended filament segment reconstruction

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

冷冻电镜 EM 3D