SAXSdb — 8g41

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8g41
沉积日期 deposition_date	2023-02-08
结构标题 title	Horse liver alcohol dehydrogense His-51-Gln form complexed with NADH
关键词 keywords	alcohol dehydrogenase horse liver His-51-Gln substitution complex with NADH, 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	29.74 Å
回转半径 Rg (电子) rg_electron	29.64 Å
零角强度 I(0) i0	104354000.00
分子量 molecular_weight	81546.0 kDa
排除体积 excluded_volume	102400 Å³
包络体积 envelope_volume	119060 Å³
水化壳体积 shell_volume	34302 Å³
包络直径 envelope_diameter	110.3 Å
壳层 Rg shell_rg	35.98 Å
包络 Rg envelope_rg	29.79 Å
形状 Rg shape_rg	29.66 Å
总 Rg total_rg	30.13 Å
总原子数 total_atoms	5684
残基数 n_residues	748
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	104.5 Å
Rg (实空间) rg_real	29.89 Å
Rg 误差 (实空间) rg_real_error	1.11 Å
I(0) (实空间) i0_real	1.0440e+08
I(0) 误差 (实空间) i0_real_error	1.8720e+06
Rg (倒空间) rg_reciprocal	29.83 Å
I(0) (倒空间) i0_reciprocal	104300000.0000
解质量估计 total_estimate	0.8475
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	29.6 Å
偏度 Skewness skewness	0.500
峰度 Kurtosis kurtosis	-0.270
角度范围 angular_range	— – 0.2650 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	45860000.0000
实空间数据点数 n_real_points	54
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.721; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.859; Smooth: 0.993

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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 (6)

Entity 1 polymer

描述 description	Alcohol dehydrogenase E chain
分子量 formula_weight	39843.3 kDa
EC 编号 ec_number	1.1.1.1
突变 mutation	H51Q
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	6596

STAGKVIKCKAAVLWEEKKPFSIEEVEVAPPKAHEVRIKMVATGICRSDDQVVSGTLVTPLPVIAGHEAAGIVESIGEGVTTVRPGDKVIPLFTPQCGKCRVCKHPEGNFCLKNDLSMPRGTMQDGTSRFTCRGKPIHHFLGTSTFSQYTVVDEISVAKIDAASPLEKVCLIGCGFSTGYGSAVKVAKVTQGSTCAVFGLGGVGLSVIMGCKAAGAARIIGVDINKDKFAKAKEVGATECVNPQDYKKPIQEVLTEMSNGGVDFSFEVIGRLDTMVTALSCCQEAYGVSVIVGVPPDSQNLSMNPMLLLSGRTWKGAIFGGFKSKDSVPKLVADFMAKKFALDPLITHVLPFEKINEGFDLLRSGESIRTILTF

来源 Source

来源生物 organism	Equus caballus
通用名 common_name	horse
NCBI 分类编号 ncbi_taxonomy_id	9796
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 3 non-polymer

描述 description	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
分子量 formula_weight	665.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 non-polymer

描述 description	(4S)-2-METHYL-2,4-PENTANEDIOL
分子量 formula_weight	118.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 5 non-polymer

描述 description	(4R)-2-METHYLPENTANE-2,4-DIOL
分子量 formula_weight	118.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 6 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	663

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6. 折叠分类 (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

结构域编号 domain_id	8g41A01
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	8g41B01
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 (7)

Histidine-51 facilitates deprotonatation of the zinc-bound ligand during catalysis by horse liver alcohol dehydrogenase

To Be Published

PRIMARY

Solvent isotope and mutagenesis studies on the proton relay system in yeast alcohol dehydrogenase 1.

Chem.Biol.Interact. (2024)

PMID: 38151107 · DOI: 10.1016/j.cbi.2023.110853

Horse Liver Alcohol Dehydrogenase: Zinc Coordination and Catalysis.

Biochemistry (2017)

PMID: 28640600 · DOI: 10.1038/355472a0

;Atomic-resolution structures of horse liver alcohol dehydrogenase with NAD(+) and fluoroalcohols define strained Michaelis complexes. ;

Biochemistry (2012)

PMID: 22531044 · DOI: 10.1021/bi300378n

Participation of histidine-51 in catalysis by horse liver alcohol dehydrogenase.

Biochemistry (2004)

PMID: 15023053 · DOI: 10.1021/bi036103m

Proton Transfer In The Mechanism Of Horse Liver Alcohol Dehydrogenase

Ph.D. Thesis (2004)

Control of coenzyme binding to horse liver alcohol dehydrogenase.

Biochemistry (1999)

PMID: 10493806 · DOI: 10.1021/bi991306p

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晶胞边长 a length_a	44.060 Å
晶胞边长 b length_b	51.320 Å
晶胞边长 c length_c	92.750 Å
晶胞夹角 α angle_alpha	91.90 °
晶胞夹角 β angle_beta	103.08 °
晶胞夹角 γ angle_gamma	109.89 °
晶胞分子数 Z z_pdb	2

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

分辨率 resolution	1.500 Å
最低分辨率 resolution_low	19.910 Å
R 因子 r_factor	0.1555
R_work r_work	0.1551
R_free r_free	0.1772

fit	/app/data/saxs_computation/g4/8g41/8g41.fit
pddf	/app/data/pr_computation/g4/8g41/8g41.pr.out
profile	/app/data/saxs_computation/g4/8g41/8g41.dat

Horse liver alcohol dehydrogense His-51-Gln form complexed with NADH

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