SAXSdb — 1grb

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1grb
沉积日期 deposition_date	1992-12-15
结构标题 title	;SUBSTRATE BINDING AND CATALYSIS BY GLUTATHIONE REDUCTASE AS DERIVED FROM REFINED ENZYME: SUBSTRATE CRYSTAL STRUCTURES AT 2 ANGSTROMS RESOLUTION ;
关键词 keywords	OXIDOREDUCTASE(FLAVOENZYME), 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	24.50 Å
回转半径 Rg (电子) rg_electron	23.76 Å
零角强度 I(0) i0	47885600.00
分子量 molecular_weight	52203.0 kDa
排除体积 excluded_volume	64817 Å³
包络体积 envelope_volume	78617 Å³
水化壳体积 shell_volume	27213 Å³
包络直径 envelope_diameter	78.1 Å
壳层 Rg shell_rg	31.26 Å
包络 Rg envelope_rg	24.03 Å
形状 Rg shape_rg	23.78 Å
总 Rg total_rg	24.56 Å
总原子数 total_atoms	3649
残基数 n_residues	461
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	77.2 Å
Rg (实空间) rg_real	24.38 Å
Rg 误差 (实空间) rg_real_error	0.45 Å
I(0) (实空间) i0_real	4.7890e+07
I(0) 误差 (实空间) i0_real_error	6.8820e+05
Rg (倒空间) rg_reciprocal	24.41 Å
I(0) (倒空间) i0_reciprocal	47890000.0000
解质量估计 total_estimate	0.9077
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	30.6 Å
偏度 Skewness skewness	0.163
峰度 Kurtosis kurtosis	-0.548
角度范围 angular_range	— – 0.3250 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	9045000.0000
实空间数据点数 n_real_points	64
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.933; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.998

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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	GLUTATHIONE REDUCTASE
分子量 formula_weight	51636.2 kDa
EC 编号 ec_number	1.6.4.2
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	4176

ACRQEPQPQGPPPAAGAVASYDYLVIGGGSGGLASARRAAELGARAAVVESHKLGGTCVNVGCVPKKVMWNTAVHSEFMHDHADYGFPSCEGKFNWRVIKEKRDAYVSRLNAIYQNNLTKSHIEIIRGHAAFTSDPKPTIEVSGKKYTAPHILIATGGMPSTPHESQIPGASLGITSDGFFQLEELPGRSVIVGAGYIAVEMAGILSALGSKTSLMIRHDKVLRSFDSMISTNCTEELENAGVEVLKFSQVKEVKKTLSGLEVSMVTAVPGRLPVMTMIPDVDCLLWAIGRVPNTKDLSLNKLGIQTDDKGHIIVDEFQNTNVKGIYAVGDVCGKALLTPVAIAAGRKLAHRLFEYKEDSKLDYNNIPTVVFSHPPIGTVGLTEDEAIHKYGIENVKTYSTSFTPMYHAVTKRKTKCVMKMVCANKEEKVVGIHMQGLGCDEMLQGFAVAVKMGATKADFDNTVAIHPTSSEELVTLR

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

Entity 2 non-polymer

描述 description	PHOSPHATE ION
分子量 formula_weight	95.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 3 non-polymer

描述 description	FLAVIN-ADENINE DINUCLEOTIDE
分子量 formula_weight	785.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 4 non-polymer

描述 description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
分子量 formula_weight	663.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 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	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	527

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6. 折叠分类 (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

结构域编号 domain_id	d1grba1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.3 — FAD/NAD(P)-binding domain
超家族 Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
家族 Family family	c.3.1.5 — FAD/NAD-linked reductases, N-terminal and central domains

结构域编号 domain_id	d1grba2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.3 — FAD/NAD(P)-binding domain
超家族 Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
家族 Family family	c.3.1.5 — FAD/NAD-linked reductases, N-terminal and central domains

结构域编号 domain_id	d1grba3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.87 — CO dehydrogenase flavoprotein C-domain-like
超家族 Superfamily superfamily	d.87.1 — FAD/NAD-linked reductases, dimerisation (C-terminal) domain
家族 Family family	d.87.1.1 — FAD/NAD-linked reductases, dimerisation (C-terminal) domain

CATH v4.4 (3 domains)

结构域编号 domain_id	1grbA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	50 — FAD/NAD(P)-binding domain
同源超家族 H-superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

结构域编号 domain_id	1grbA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	50 — FAD/NAD(P)-binding domain
同源超家族 H-superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

结构域编号 domain_id	1grbA03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	390 — Enolase-like; domain 1
同源超家族 H-superfamily homologous superfamily	30 — FAD/NAD-linked reductase, C-terminal dimerisation domain

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7. 引用文献 (14)

;Substrate binding and catalysis by glutathione reductase as derived from refined enzyme: substrate crystal structures at 2 A resolution. ;

J.Mol.Biol. (1989)

PMID: 2585516 · DOI: 10.1016/0022-2836(89)90298-2 PRIMARY

;Inhibition of Human Glutathione Reductase by the Nitrosourea Drugs 1,3-Bis(2-Chloroethyl)-1-Nitrosourea and 1-(2-Chloroethyl)-3-(2-Hydroxyethyl)-1-Nitrosourea ;

Eur.J.Biochem. (1988)

Refined Structure of Glutathione Reductase at 1.54 Angstroms Resolution

J.Mol.Biol. (1987)

Interaction of a Glutathione S-Conjugate with Glutathione Reductase. Kinetic and X-Ray Crystallographic Studies

Eur.J.Biochem. (1984)

;Comparison of the Three-Dimensional Protein and Nucleotide Structure of the Fad-Binding Domain of P-Hydroxybenzoate Hydroxylase with the Fad-as Well as Nadph-Binding Domains of Glutathione Reductase ;

J.Mol.Biol. (1983)

The Catalytic Mechanism of Glutathione Reductase as Derived from X-Ray Diffraction Analyses of Reaction Intermediates

J.Biol.Chem. (1983)

Fad-Binding Site of Glutathione Reductase

J.Mol.Biol. (1982)

Glutathione Reductase from Human Erythrocytes. The Sequences of the Nadph Domain and of the Interface Domain

Eur.J.Biochem. (1982)

Three-Dimensional Structure of Glutathione Reductase at 2 Angstroms Resolution

J.Mol.Biol. (1981)

Gene Duplication in Glutathione Reductase

J.Mol.Biol. (1980)

The C-Terminal Fragment of Human Glutathione Reductase Contains the Postulated Catalytic Histidine

FEBS Lett. (1979)

The Structure of the Flavoenzyme Glutathione Reductase

Nature (1978)

Low Resolution Structure of Human Erythrocyte Glutathione Reductase

J.Mol.Biol. (1977)

Crystals of Human Erythrocyte Glutathione Reductase

FEBS Lett. (1975)

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晶胞边长 a length_a	119.800 Å
晶胞边长 b length_b	84.500 Å
晶胞边长 c length_c	63.200 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	58.70 °
晶胞分子数 Z z_pdb	4

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

分辨率 resolution	1.850 Å
最低分辨率 resolution_low	10.000 Å
R 因子 r_factor	0.1620
R_work r_work	—
R_free r_free	—

fit	/app/data/saxs_computation/gr/1grb/1grb.fit
pddf	/app/data/pr_computation/gr/1grb/1grb.pr.out
profile	/app/data/saxs_computation/gr/1grb/1grb.dat

;SUBSTRATE BINDING AND CATALYSIS BY GLUTATHIONE REDUCTASE AS DERIVED FROM REFINED ENZYME: SUBSTRATE CRYSTAL STRUCTURES AT 2 ANGSTROMS RESOLUTION ;

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution