2gm9

Structure of rabbit muscle glycogen phosphorylase in complex with thienopyrrole

Method: X-RAY DIFFRACTION D_max: 93.0 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	2gm9
沉积日期 deposition_date	2006-04-06
结构标题 title	Structure of rabbit muscle glycogen phosphorylase in complex with thienopyrrole
关键词 keywords	GLYCOGEN PHOSPHORYLASE, 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	28.17 Å
回转半径 Rg (电子) rg_electron	27.13 Å
零角强度 I(0) i0	137433000.00
分子量 molecular_weight	93369.0 kDa
排除体积 excluded_volume	117120 Å³
包络体积 envelope_volume	136510 Å³
水化壳体积 shell_volume	40215 Å³
包络直径 envelope_diameter	95.4 Å
壳层 Rg shell_rg	36.02 Å
包络 Rg envelope_rg	27.42 Å
形状 Rg shape_rg	27.14 Å
总 Rg total_rg	27.93 Å
总原子数 total_atoms	6583
残基数 n_residues	805
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	93.0 Å
Rg (实空间) rg_real	28.58 Å
Rg 误差 (实空间) rg_real_error	0.23 Å
I(0) (实空间) i0_real	1.3530e+08
I(0) 误差 (实空间) i0_real_error	1.5810e+06
Rg (倒空间) rg_reciprocal	28.06 Å
I(0) (倒空间) i0_reciprocal	137400000.0000
解质量估计 total_estimate	0.7020
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	34.9 Å
偏度 Skewness skewness	0.313
峰度 Kurtosis kurtosis	-0.219
角度范围 angular_range	— – 0.2800 Å⁻¹
当前正则化参数 α current_alpha	4.3860
最高正则化参数 α highest_alpha	42320000.0000
实空间数据点数 n_real_points	57
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.861; Stabil: 0.927; Sysdev: 0.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.786

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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	Glycogen phosphorylase, muscle form
分子量 formula_weight	95280.9 kDa
EC 编号 ec_number	2.4.1.1
来源方法 src_method	nat
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	7052

QISVRGLAGVENVTELKKNFNRHLHFTLVKDRNVATPRDYYFALAHTVRDHLVGRWIRTQQHYYEKDPKRIYYLSLEFYMGRTLQNTMVNLALENACDEATYQLGLDMEELEEIEEDAGLGNGGLGRLAACFLDSMATLGLAAYGYGIRYEFGIFNQKICGGWQMEEADDWLRYGNPWEKARPEFTLPVHFYGRVEHTSQGAKWVDTQVVLAMPYDTPVPGYRNNVVNTMRLWSAKAPNDFNLKDFNVGGYIQAVLDRNLAENISRVLYPNDNFFEGKELRLKQEYFVVAATLQDIIRRFKSSKFGCRDPVRTNFDAFPDKVAIQLNDTHPSLAIPELMRVLVDLERLDWDKAWEVTVKTCAYTNHTVLPEALERWPVHLLETLLPRHLQIIYEINQRFLNRVAAAFPGDVDRLRRMSLVEEGAVKRINMAHLCIAGSHAVNGVARIHSEILKKTIFKDFYELEPHKFQNKTNGITPRRWLVLCNPGLAEIIAERIGEEYISDLDQLRKLLSYVDDEAFIRDVAKVKQENKLKFAAYLEREYKVHINPNSLFDVQVKRIHEYKRQLLNCLHVITLYNRIKKEPNKFVVPRTVMIGGKAAPGYHMAKMIIKLITAIGDVVNHDPVVGDRLRVIFLENYRVSLAEKVIPAADLSEQISTAGTEASGTGNMKFMLNGALTIGTMDGANVEMAEEAGEENFFIFGMRVEDVDRLDQRGYNAQEYYDRIPELRQIIEQLSSGFFSPKQPDLFKDIVNMLMHHDRFKVFADYEEYVKCQERVSALYKNPREWTRMVIRNIATSGKFSSDRTIAQYAREIWGVEPSRQRLPA

Entity 2 non-polymer

描述 description	(5-HYDROXY-4,6-DIMETHYLPYRIDIN-3-YL)METHYL DIHYDROGEN PHOSPHATE
分子量 formula_weight	233.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 3 non-polymer

描述 description	2-CHLORO-N-[(3R)-2-OXO-1,2,3,4-TETRAHYDROQUINOLIN-3-YL]-6H-THIENO[2,3-B]PYRROLE-5-CARBOXAMIDE
分子量 formula_weight	345.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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	455

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6. 折叠分类 (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

结构域编号 domain_id	d2gm9a_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.87 — UDP-Glycosyltransferase/glycogen phosphorylase
超家族 Superfamily superfamily	c.87.1 — UDP-Glycosyltransferase/glycogen phosphorylase
家族 Family family	c.87.1.4 — Oligosaccharide phosphorylase

CATH v4.4 (2 domains)

结构域编号 domain_id	2gm9A01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	2000 — Glycogen Phosphorylase B;

结构域编号 domain_id	2gm9A02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	2000 — Glycogen Phosphorylase B;

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7. 引用文献 (1)

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晶胞边长 a length_a	126.781 Å
晶胞边长 b length_b	126.781 Å
晶胞边长 c length_c	115.144 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 43 21 2
空间群编号 int_tables_number	96
晶系 crystal_system	—

分辨率 resolution	2.300 Å
最低分辨率 resolution_low	91.290 Å
R 因子 r_factor	0.1856
R_work r_work	0.1825
R_free r_free	0.2451

fit	/app/data/saxs_computation/gm/2gm9/2gm9.fit
pddf	/app/data/pr_computation/gm/2gm9/2gm9.pr.out
profile	/app/data/saxs_computation/gm/2gm9/2gm9.dat