9iwd

;High Resolution Crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase from Saccharomyces cerevisiae Complexed with a Maleate Derivative ;

Method: X-RAY DIFFRACTION D_max: 70.6 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	9iwd
沉积日期 deposition_date	2024-07-25
最后修订 last_revision	2025-08-06
结构标题 title	;High Resolution Crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase from Saccharomyces cerevisiae Complexed with a Maleate Derivative ;
关键词 keywords	covalent inhibitor, PROTEIN BINDING; PROTEIN BINDING
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	20.98 Å
回转半径 Rg (电子) rg_electron	20.29 Å
零角强度 I(0) i0	40011100.00
分子量 molecular_weight	32634.0 kDa
排除体积 excluded_volume	31485 Å³
包络体积 envelope_volume	52013 Å³
水化壳体积 shell_volume	21441 Å³
包络直径 envelope_diameter	73.6 Å
壳层 Rg shell_rg	26.83 Å
包络 Rg envelope_rg	20.51 Å
形状 Rg shape_rg	20.29 Å
总 Rg total_rg	20.91 Å
总原子数 total_atoms	2472
残基数 n_residues	323
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	70.6 Å
Rg (实空间) rg_real	20.92 Å
Rg 误差 (实空间) rg_real_error	0.47 Å
I(0) (实空间) i0_real	4.0010e+07
I(0) 误差 (实空间) i0_real_error	5.2250e+05
Rg (倒空间) rg_reciprocal	20.93 Å
I(0) (倒空间) i0_reciprocal	40010000.0000
解质量估计 total_estimate	0.6149
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	24.5 Å
偏度 Skewness skewness	0.303
峰度 Kurtosis kurtosis	-0.310
角度范围 angular_range	— – 0.3800 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	6765000.0000
实空间数据点数 n_real_points	70
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.822; Stabil: 1.000; Sysdev: 0.177; Positv: 1.000; Valcen: 0.993; Smooth: 0.000

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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	Glyceraldehyde-3-phosphate dehydrogenase 3
分子量 formula_weight	36808.7 kDa
EC 编号 ec_number	1.2.1.12
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	2608

MGHHHHHHMVRVAINGFGRIGRLVMRIALSRPNVEVVALNDPFITNDYAAYMFKYDSTHGRYAGEVSHDDKHIIVDGKKIATYQERDPANLPWGSSNVDIAIDSTGVFKELDTAQKHIDAGAKKVVITAPSSTAPMFVMGVNEEKYTSDLKIVSNASCTTNCLAPLAKVINDAFGIEEGLMTTVHSLTATQKTVDGPSHKDWRGGRTASGNIIPSSTGAAKAVGKVLPELQGKLTGMAFRVPTVDVSVVDLTVKLNKETTYDEIKKVVKAAAEGKLKGVLGYTEDAVVSSDFLGDSHSSIFDASAGIQLSPKFVKLVSWYDNEYGYSTRVVDLVEHVAKA

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;Baker's yeast ;
NCBI 分类编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

描述 description	ethyl 4-[(4-chlorophenyl)amino]-4-oxidanylidene-butanoate
分子量 formula_weight	255.7 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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	2

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	136

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7. 引用文献 (1)

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晶胞边长 a length_a	116.455 Å
晶胞边长 b length_b	116.455 Å
晶胞边长 c length_c	112.627 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	16

空间群 space_group	I 41 2 2
空间群编号 int_tables_number	98
晶系 crystal_system	—

分辨率 resolution	2.070 Å
最低分辨率 resolution_low	19.970 Å
R 因子 r_factor	0.1870
R_work r_work	0.1848
R_free r_free	0.2269

fit	/app/data/saxs_computation/iw/9iwd/9iwd.fit
pddf	/app/data/pr_computation/iw/9iwd/9iwd.pr.out
profile	/app/data/saxs_computation/iw/9iwd/9iwd.dat

;High Resolution Crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase from Saccharomyces cerevisiae Complexed with a Maleate Derivative ;

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