SAXSdb — 1nel

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1nel
沉积日期 deposition_date	1993-08-20
结构标题 title	FLUORIDE INHIBITION OF YEAST ENOLASE: CRYSTAL STRUCTURE OF THE ENOLASE-MG2+-F--PI COMPLEX AT 2.6-ANGSTROMS RESOLUTION
关键词 keywords	CARBON-OXYGEN LYASE; CARBON-OXYGEN LYASE
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	22.08 Å
回转半径 Rg (电子) rg_electron	21.19 Å
零角强度 I(0) i0	36496400.00
分子量 molecular_weight	46762.0 kDa
排除体积 excluded_volume	58574 Å³
包络体积 envelope_volume	65961 Å³
水化壳体积 shell_volume	25407 Å³
包络直径 envelope_diameter	72.2 Å
壳层 Rg shell_rg	28.55 Å
包络 Rg envelope_rg	21.49 Å
形状 Rg shape_rg	21.18 Å
总 Rg total_rg	22.07 Å
总原子数 total_atoms	3296
残基数 n_residues	436
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	70.2 Å
Rg (实空间) rg_real	21.96 Å
Rg 误差 (实空间) rg_real_error	0.33 Å
I(0) (实空间) i0_real	3.6500e+07
I(0) 误差 (实空间) i0_real_error	4.7290e+05
Rg (倒空间) rg_reciprocal	21.98 Å
I(0) (倒空间) i0_reciprocal	36500000.0000
解质量估计 total_estimate	0.8951
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	27.2 Å
偏度 Skewness skewness	0.227
峰度 Kurtosis kurtosis	-0.358
角度范围 angular_range	— – 0.3600 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	7240000.0000
实空间数据点数 n_real_points	68
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.881; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.990

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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	ENOLASE
分子量 formula_weight	46690.7 kDa
EC 编号 ec_number	4.2.1.11
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	3570

AVSKVYARSVYDSRGNPTVEVELTTEKGVFRSIVPSGASTGVHEALEMRDGDKSKWMGKGVLHAVKNVNDVIAPAFVKANIDVSDQKAVDDFLISLDGTANKSKLGANAILGVSLAASRAAAAEKNVPLYKHLADLSKSKTSPYVLPVPFLNVLNGGSHAGGALALQEFMIAPTGAKTFAEALRIGSEVYHNLKSLTKKRYGASAGNVGDEGGVAPNIQTAEEALDLIVDAIKAAGHDGKVKIGLDCASSEFFKDGKYDLDFKNPNSDKSKWLTGPQLADLYHSLMKRYPIVSIEDPFAEDDWEAWSHFFKTAGIQIVADDLTVTNPKRIATAIEKKAADALLLKVNQIGTLSESIKAAQDSFAAGWGVMVSHRSGETEDTFIADLVVGLRTGQIKTGAPARSERLAKLNQLLRIEEELGDNAVFAGENFHHGDKL

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	4932

Entity 2 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 3 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 4 non-polymer

描述 description	FLUORIDE ION
分子量 formula_weight	19.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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	274

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6. 折叠分类 (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d1nela1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.11 — Enolase C-terminal domain-like
家族 Family family	c.1.11.1 — Enolase

结构域编号 domain_id	d1nela2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.54 — Enolase N-terminal domain-like
超家族 Superfamily superfamily	d.54.1 — Enolase N-terminal domain-like
家族 Family family	d.54.1.1 — Enolase N-terminal domain-like

CATH v4.4 (2 domains)

结构域编号 domain_id	1nelA01
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	10 — Enolase-like, N-terminal domain

结构域编号 domain_id	1nelA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	120 — Enolase-like C-terminal domain

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7. 引用文献 (8)

Fluoride inhibition of yeast enolase: crystal structure of the enolase-Mg(2+)-F(-)-Pi complex at 2.6 A resolution.

Proteins (1993)

PMID: 8346189 · DOI: 10.1002/prot.340160302 PRIMARY

;Mechanism of Enolase: The Crystal Structure of Enolase-Mg2+-Phosphoglycerate(Slash) Phosphoenolpyruvate Complex at 2.2-Angstroms Resolution ;

Biochemistry (1991)

;Inhibition of Enolase: The Crystal Structures of Enolase-Ca2+-Phosphoglycerate and Enolase-Zn2+-Phosphoglycolate Complexes at 2.2-Angstroms Resolution ;

Biochemistry (1991)

Refined Structure of Yeast Apo-Enolase at 2.25 Angstroms Resolution

J.Mol.Biol. (1990)

Crystal Structure of Holoenzyme Refined at 1.9 Angstroms Resolution: Trigonal-Bipyramidal Geometry of the Cation Binding Site

J.Am.Chem.Soc. (1989)

;The Structure of Yeast Enolase at 2.25-Angstroms Resolution. An 8-Fold Beta+Alpha-Barrel with a Novel Beta Beta Alpha Alpha (Beta Alpha)6 Topology ;

J.Biol.Chem. (1989)

Crystal Structure of Enolase Indicates that Enolase and Pyruvate Kinase Evolved from a Common Ancestor

Nature (1988)

Crystallization and Preliminary Crystallographic Data for a Tetragonal Form of Yeast Enolase

J.Mol.Biol. (1984)

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晶胞边长 a length_a	122.500 Å
晶胞边长 b length_b	122.500 Å
晶胞边长 c length_c	67.000 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 42 21 2
空间群编号 int_tables_number	94
晶系 crystal_system	—

分辨率 resolution	2.600 Å
最低分辨率 resolution_low	— Å
R 因子 r_factor	0.1690
R_work r_work	—
R_free r_free	—

fit	/app/data/saxs_computation/ne/1nel/1nel.fit
pddf	/app/data/pr_computation/ne/1nel/1nel.pr.out
profile	/app/data/saxs_computation/ne/1nel/1nel.dat

FLUORIDE INHIBITION OF YEAST ENOLASE: CRYSTAL STRUCTURE OF THE ENOLASE-MG2+-F--PI COMPLEX AT 2.6-ANGSTROMS RESOLUTION

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution