SAXSdb — 2gcg

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2gcg
沉积日期 deposition_date	2006-03-14
结构标题 title	Ternary Crystal Structure of Human Glyoxylate Reductase/Hydroxypyruvate Reductase
关键词 keywords	NAD(P) Rossmann Fold, Formate/Glycerate Dehydrogenase Substrate-Binding Domain, Oxidoreductase; OXIDOREDUCTASE
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	41.49 Å
回转半径 Rg (电子) rg_electron	41.07 Å
零角强度 I(0) i0	315623000.00
分子量 molecular_weight	144040.0 kDa
排除体积 excluded_volume	179880 Å³
包络体积 envelope_volume	236110 Å³
水化壳体积 shell_volume	47753 Å³
包络直径 envelope_diameter	126.1 Å
壳层 Rg shell_rg	46.53 Å
包络 Rg envelope_rg	40.33 Å
形状 Rg shape_rg	41.06 Å
总 Rg total_rg	41.35 Å
总原子数 total_atoms	10090
残基数 n_residues	1294
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	126.7 Å
Rg (实空间) rg_real	41.44 Å
Rg 误差 (实空间) rg_real_error	1.02 Å
I(0) (实空间) i0_real	3.1560e+08
I(0) 误差 (实空间) i0_real_error	5.6970e+06
Rg (倒空间) rg_reciprocal	41.49 Å
I(0) (倒空间) i0_reciprocal	315600000.0000
解质量估计 total_estimate	0.8808
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	33.3 Å
偏度 Skewness skewness	0.097
峰度 Kurtosis kurtosis	-0.922
角度范围 angular_range	— – 0.1900 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	34480000.0000
实空间数据点数 n_real_points	39
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.928; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.969; Smooth: 0.694

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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	Glyoxylate reductase/hydroxypyruvate reductase
分子量 formula_weight	35869.4 kDa
EC 编号 ec_number	1.1.1.79
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	10701

ASMRPVRLMKVFVTRRIPAEGRVALARAADCEVEQWDSDEPIPAKELERGVAGAHGLLCLLSDHVDKRILDAAGANLKVISTMSVGIDHLALDEIKKRGIRVGYTPDVLTDTTAELAVSLLLTTCRRLPEAIEEVKNGGWTSWKPLWLCGYGLTQSTVGIIGLGRIGQAIARRLKPFGVQRFLYTGRQPRPEEAAEFQAEFVSTPELAAQSDFIVVACSLTPATEGLCNKDFFQKMKETAVFINISRGDVVNQDDLYQALASGKIAAAGLDVTSPEPLPTNHPLLTLKNCVILPHIGSATHRTRNTMSLLAANNLLAGLRGEPMPSELKL

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	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
分子量 formula_weight	745.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 3 non-polymer

描述 description	(2R)-2,3-DIHYDROXYPROPANOIC ACID
分子量 formula_weight	106.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 non-polymer

描述 description	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	5

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	611

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6. 折叠分类 (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

结构域编号 domain_id	2gcgA01
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	720 — NAD(P)-binding Rossmann-like Domain

结构域编号 domain_id	2gcgA02
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	720 — NAD(P)-binding Rossmann-like Domain

结构域编号 domain_id	2gcgB01
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	720 — NAD(P)-binding Rossmann-like Domain

结构域编号 domain_id	2gcgB02
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	720 — NAD(P)-binding Rossmann-like Domain

结构域编号 domain_id	2gcgC01
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	720 — NAD(P)-binding Rossmann-like Domain

结构域编号 domain_id	2gcgC02
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	720 — NAD(P)-binding Rossmann-like Domain

结构域编号 domain_id	2gcgD01
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	720 — NAD(P)-binding Rossmann-like Domain

结构域编号 domain_id	2gcgD02
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	720 — NAD(P)-binding Rossmann-like Domain

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7. 引用文献 (1)

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晶胞边长 a length_a	76.568 Å
晶胞边长 b length_b	66.877 Å
晶胞边长 c length_c	149.780 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	98.22 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	—

分辨率 resolution	2.200 Å
最低分辨率 resolution_low	46.200 Å
R 因子 r_factor	0.2050
R_work r_work	0.2010
R_free r_free	0.2820

fit	/app/data/saxs_computation/gc/2gcg/2gcg.fit
pddf	/app/data/pr_computation/gc/2gcg/2gcg.pr.out
profile	/app/data/saxs_computation/gc/2gcg/2gcg.dat

Ternary Crystal Structure of Human Glyoxylate Reductase/Hydroxypyruvate Reductase

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