9nal

;Cryo-EM structure of ternary complex of human phosphoribosylglycinamidine synthase with the intermediate (iminophosphate) and ADP bound at the synthase site. ;

Method: ELECTRON MICROSCOPY D_max: 92.3 Å Quality: REASONABLE

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	9nal
沉积日期 deposition_date	2025-02-12
结构标题 title	;Cryo-EM structure of ternary complex of human phosphoribosylglycinamidine synthase with the intermediate (iminophosphate) and ADP bound at the synthase site. ;
关键词 keywords	iminophosphate ADP human phosphoribosylglycinamidine synthase, LIGASE; LIGASE
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	30.52 Å
回转半径 Rg (电子) rg_electron	29.84 Å
零角强度 I(0) i0	554319000.00
分子量 molecular_weight	124790.0 kDa
排除体积 excluded_volume	119680 Å³
包络体积 envelope_volume	198640 Å³
水化壳体积 shell_volume	51975 Å³
包络直径 envelope_diameter	98.1 Å
壳层 Rg shell_rg	39.55 Å
包络 Rg envelope_rg	30.02 Å
形状 Rg shape_rg	29.87 Å
总 Rg total_rg	30.35 Å
总原子数 total_atoms	9448
残基数 n_residues	1287
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	92.3 Å
Rg (实空间) rg_real	30.32 Å
Rg 误差 (实空间) rg_real_error	0.50 Å
I(0) (实空间) i0_real	5.5430e+08
I(0) 误差 (实空间) i0_real_error	9.1990e+06
Rg (倒空间) rg_reciprocal	30.41 Å
I(0) (倒空间) i0_reciprocal	554400000.0000
解质量估计 total_estimate	0.6894
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	39.0 Å
偏度 Skewness skewness	0.135
峰度 Kurtosis kurtosis	-0.508
角度范围 angular_range	— – 0.2600 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	119400000.0000
实空间数据点数 n_real_points	53
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.935; Stabil: 1.000; Sysdev: 0.077; Positv: 1.000; Valcen: 0.977; Smooth: 0.944

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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	Phosphoribosylformylglycinamidine synthase
分子量 formula_weight	148495.7 kDa
EC 编号 ec_number	6.3.5.3
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	9590

MSPVLHFYVRPSGHEGAAPGHTRRKLQGKLPELQGVETELCYNVNWTAEALPSAEETKKLMWLFGCPLLLDDVARESWLLPGSNDLLLEVGPRLNFSTPTSTNIVSVCRATGLGPVDRVETTRRYRLSFAHPPSAEVEAIALATLHDRMTEQHFPHPIQSFSPESMPEPLNGPINILGEGRLALEKANQELGLALDSWDLDFYTKRFQELQRNPSTVEAFDLAQSNSEHSRHWFFKGQLHVDGQKLVHSLFESIMSTQESSNPNNVLKFCDNSSAIQGKEVRFLRPEDPTRPSRFQQQQGLRHVVFTAETHNFPTGVCPFSGATTGTGGRIRDVQCTGRGAHVVAGTAGYCFGNLHIPGYNLPWEDPSFQYPGNFARPLEVAIEASNGASDYGNKFGEPVLAGFARSLGLQLPDGQRREWIKPIMFSGGIGSMEADHISKEAPEPGMEVVKVGGPVYRIGVGGGAASSVQVQGDNTSDLDFGAVQRGDPEMEQKMNRVIRACVEAPKGNPICSLHDQGAGGNGNVLKELSDPAGAIIYTSRFQLGDPTLNALEIWGAEYQESNALLLRSPNRDFLTHVSARERCPACFVGTITGDRRIVLVDDRECPVRRNGQGDAPPTPLPTPVDLELEWVLGKMPRKEFFLQRKPPMLQPLALPPGLSVHQALERVLRLPAVASKRYLTNKVDRSVGGLVAQQQCVGPLQTPLADVAVVALSHEELIGAATALGEQPVKSLLDPKVAARLAVAEALTNLVFALVTDLRDVKCSGNWMWAAKLPGEGAALADACEAMVAVMAALGVAVDGGKDSLSMAARVGTETVRAPGSLVISAYAVCPDITATVTPDLKHPEGRGHLLYVALSPGQHRLGGTALAQCFSQLGEHPPDLDLPENLVRAFSITQGLLKDRLLCSGHDVSDGGLVTCLLEMAFAGNCGLQVDVPVPRVDVLSVLFAEEPGLVLEVQEPDLAQVLKRYRDAGLHCLELGHTGEAGPHAMVRVSVNGAVVLEEPVGELRALWEETSFQLDRLQAEPRCVAEEERGLRERMGPSYCLPPTFPKASVPREPGGPSPRVAILREEGSNGDREMADAFHLAGFEVWDVTMQDLCSGAIGLDTFRGVAFVGGFSYADVLGSAKGWAAAVTFHPRAGAELRRFRKRPDTFSLGVCNGCQLLALLGWVGGDPNEDAAEMGPDSQPARPGLLLRHNLSGRYESRWASVRVGPGPALMLRGMEGAVLPVWSAHGEGYVAFSSPELQAQIEARGLAPLHWADDDGNPTEQYPLNPNGSPGGVAGICSCDGRHLAVMPHPERAVRPWQWAWRPPPFDTLTTSPWLQLFINARNWTLEGSCTRTRPLEQKLISEEDLAANDILDYKDDDDKV

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	Homo sapiens

Entity 2 non-polymer

描述 description	ADENOSINE-5'-DIPHOSPHATE
分子量 formula_weight	427.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 3 non-polymer

描述 description	N-[2-formamido-1-(phosphonooxy)ethylidene]-5-O-phosphono-beta-D-ribofuranosylamine
分子量 formula_weight	394.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 4 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	3

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	96

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7. 引用文献 (1)

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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	3.220 Å
最低分辨率 resolution_low	— Å
R 因子 r_factor	—
R_work r_work	—
R_free r_free	—

分辨率 resolution	3.22 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	110648

fit	/app/data/saxs_computation/na/9nal/9nal.fit
pddf	/app/data/pr_computation/na/9nal/9nal.pr.out
profile	/app/data/saxs_computation/na/9nal/9nal.dat

;Cryo-EM structure of ternary complex of human phosphoribosylglycinamidine synthase with the intermediate (iminophosphate) and ADP bound at the synthase site. ;

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

精修参数 Refinement

冷冻电镜 EM 3D