8r4g

Plastidial phosphorylase Pho1 from Solanum tuberosum in complex with a-D-glucose

Method: X-RAY DIFFRACTION D_max: 150.2 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	8r4g
沉积日期 deposition_date	2023-11-13
结构标题 title	Plastidial phosphorylase Pho1 from Solanum tuberosum in complex with a-D-glucose
关键词 keywords	Glycosyltransferase, Carbohydrate metabolism, TRANSFERASE; TRANSFERASE
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	45.23 Å
回转半径 Rg (电子) rg_electron	44.81 Å
零角强度 I(0) i0	1142020000.00
分子量 molecular_weight	284660.0 kDa
排除体积 excluded_volume	357610 Å³
包络体积 envelope_volume	449990 Å³
水化壳体积 shell_volume	81390 Å³
包络直径 envelope_diameter	165.8 Å
壳层 Rg shell_rg	50.91 Å
包络 Rg envelope_rg	44.88 Å
形状 Rg shape_rg	44.80 Å
总 Rg total_rg	45.09 Å
总原子数 total_atoms	20082
残基数 n_residues	2487
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	150.2 Å
Rg (实空间) rg_real	45.17 Å
Rg 误差 (实空间) rg_real_error	1.15 Å
I(0) (实空间) i0_real	1.1420e+09
I(0) 误差 (实空间) i0_real_error	1.8970e+07
Rg (倒空间) rg_reciprocal	45.23 Å
I(0) (倒空间) i0_reciprocal	1142000000.0000
解质量估计 total_estimate	0.8853
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	51.5 Å
偏度 Skewness skewness	0.288
峰度 Kurtosis kurtosis	-0.428
角度范围 angular_range	— – 0.1750 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	238300000.0000
实空间数据点数 n_real_points	36
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.886; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.850

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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	Alpha-1,4 glucan phosphorylase L-1 isozyme, chloroplastic/amyloplastic
分子量 formula_weight	104008.4 kDa
EC 编号 ec_number	2.4.1.1
来源方法 src_method	nat
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C
原子数 atom_count	20212

TLSEKIHHPITEQGGESDLSSFAPDAASITSSIKYHAEFTPVFSPERFELPKAFFATAQSVRDSLLINWNATYDIYEKLNMKQAYYLSMEFLQGRALLNAIGNLELTGAFAEALKNLGHNLENVASQEPDAALGNGGLGRLASCFLDSLATLNYPAWGYGLRYKYGLFKQRITKDGQEEVAEDWLEIGSPWEVVRNDVSYPIKFYGKVSTGSDGKRYWIGGEDIKAVAYDVPIPGYKTRTTISLRLWSTQVPSADFDLSAFNAGEHTKACEAQANAEKICYILYPGDESEEGKILRLKQQYTLCSASLQDIISRFERRSGDRIKWEEFPEKVAVQMNDTHPTLCIPELMRILIDLKGLNWNEAWNITQRTVAYTNHTVLPEALEKWSYELMQKLLPRHVEIIEAIDEELVHEIVLKYGSMDLNKLEEKLTTMRILENFDLPSSVAELFIKPEISVDDDTETVEVHDKVEASDKVVTNDEDDTGKKTSVKIEAAAEKDIDKKTPVSPEPAVIPPKKVRMANLCVVGGHAVNGVAEIHSEIVKEEVFNDFYELWPEKFQNKTNGVTPRRWIRFCNPPLSAIITKWTGTEDWVLKTEKLAELQKFADNEDLQNEWREAKRSNKIKVVSFLKEKTGYSVVPDAMFDIQVKRIHEYKRQLLNIFGIVYRYKKMKEMTAAERKTNFVPRVCIFGGKAFATYVQAKRIVKFITDVGATINHDPEIGDLLKVVFVPDYNVSVAELLIPASDLSEHISTAGMEASGTSNMKFAMNGCIQIGTLDGANVEIREEVGEENFFLFGAQAHEIAGLRKERADGKFVPDERFEEVKEFVRSGAFGSYNYDDLIGSLEGNEGFGRADYFLVGKDFPSYIECQEKVDEAYRDQKRWTTMSILNTAGSYKFSSDRTIHEYAKDIWNIEAVEIA

Entity 2 non-polymer

描述 description	alpha-D-glucopyranose
分子量 formula_weight	180.2 kDa
来源方法 src_method	nat
拷贝数 entity_count	3

Entity 3 non-polymer

描述 description	GLYCEROL
分子量 formula_weight	92.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	9

Entity 4 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	130

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7. 引用文献 (1)

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晶胞边长 a length_a	218.233 Å
晶胞边长 b length_b	125.913 Å
晶胞边长 c length_c	117.075 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.05 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	12

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	—

分辨率 resolution	3.100 Å
最低分辨率 resolution_low	117.070 Å
R 因子 r_factor	0.2379
R_work r_work	0.2355
R_free r_free	0.2862

fit	/app/data/saxs_computation/r4/8r4g/8r4g.fit
pddf	/app/data/pr_computation/r4/8r4g/8r4g.pr.out
profile	/app/data/saxs_computation/r4/8r4g/8r4g.dat

Plastidial phosphorylase Pho1 from Solanum tuberosum in complex with a-D-glucose

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

衍射实验 Diffraction