1lcd

;STRUCTURE OF THE COMPLEX OF LAC REPRESSOR HEADPIECE AND AN 11 BASE-PAIR HALF-OPERATOR DETERMINED BY NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY AND RESTRAINED MOLECULAR DYNAMICS ;

Method: SOLUTION NMR D_max: 49.6 Å Quality: GOOD

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	1lcd
沉积日期 deposition_date	1993-03-25
结构标题 title	;STRUCTURE OF THE COMPLEX OF LAC REPRESSOR HEADPIECE AND AN 11 BASE-PAIR HALF-OPERATOR DETERMINED BY NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY AND RESTRAINED MOLECULAR DYNAMICS ;
关键词 keywords	GENE REGULATION/DNA, GENE REGULATION-DNA complex; GENE REGULATION/DNA
实验方法 method	SOLUTION NMR

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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	14.39 Å
回转半径 Rg (电子) rg_electron	14.07 Å
零角强度 I(0) i0	39083200.00
分子量 molecular_weight	37203.0 kDa
排除体积 excluded_volume	40983 Å³
包络体积 envelope_volume	20550 Å³
水化壳体积 shell_volume	12041 Å³
包络直径 envelope_diameter	52.1 Å
壳层 Rg shell_rg	20.16 Å
包络 Rg envelope_rg	15.17 Å
形状 Rg shape_rg	13.96 Å
总 Rg total_rg	14.71 Å
总原子数 total_atoms	2970
残基数 n_residues	219
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	49.6 Å
Rg (实空间) rg_real	14.35 Å
Rg 误差 (实空间) rg_real_error	0.38 Å
I(0) (实空间) i0_real	3.9080e+07
I(0) 误差 (实空间) i0_real_error	4.9090e+05
Rg (倒空间) rg_reciprocal	14.36 Å
I(0) (倒空间) i0_reciprocal	39080000.0000
解质量估计 total_estimate	0.7954
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	49.0 Å
偏度 Skewness skewness	0.249
峰度 Kurtosis kurtosis	-0.382
角度范围 angular_range	— – 0.5000 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	497200.0000
实空间数据点数 n_real_points	80
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.793; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.958; 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 (5)

Entity 1 polymer

描述 description	;DNA (5'-D(APAPTPTPGPTPGPAPGPCP*G)-3') ;
分子量 formula_weight	3413.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polydeoxyribonucleotide
链编号 strand_id	B
原子数 atom_count	3384

AATTGTGAGCG

Entity 2 polymer

描述 description	;DNA (5'-D(CPGPCPTPCPAPCPAPAPTP*T)-3') ;
分子量 formula_weight	3293.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polydeoxyribonucleotide
链编号 strand_id	C

CGCTCACAATT

Entity 3 polymer

描述 description	Lac Repressor
分子量 formula_weight	5693.4 kDa
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

MKPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNR

来源 Source

来源生物 organism	Escherichia coli
NCBI 分类编号 ncbi_taxonomy_id	562

Entity 4 non-polymer

描述 description	SODIUM ION
分子量 formula_weight	23.0 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	49

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6. 折叠分类 (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

结构域编号 domain_id	d1lcda_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.35 — lambda repressor-like DNA-binding domains
超家族 Superfamily superfamily	a.35.1 — lambda repressor-like DNA-binding domains
家族 Family family	a.35.1.5 — GalR/LacI-like bacterial regulator

CATH v4.4 (1 domains)

结构域编号 domain_id	1lcdA00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	260 — 434 Repressor (Amino-terminal Domain)
同源超家族 H-superfamily homologous superfamily	40 — lambda repressor-like DNA-binding domains

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7. 引用文献 (10)

;Structure of the complex of lac repressor headpiece and an 11 base-pair half-operator determined by nuclear magnetic resonance spectroscopy and restrained molecular dynamics. ;

J.Mol.Biol. (1993)

PMID: 8230225 · DOI: 10.1006/jmbi.1993.1598 PRIMARY

;Assignment of the 1H-NMR Spectrum of a Lac Repressor Headpiece-Operator Complex in H2O and Identification of Noes. Consequences for Protein-DNA Interaction ;

Eur.J.Biochem. (1990)

Two-Dimensional NMR Study of a Protein-DNA Complex. Lac Repressor Headpiece-Operator Interaction

Biochem.Pharm. (1990)

1H NMR Study of a Complex between the Lac Repressor Headpiece and a 22 Base Pair Symmetric Lac Operator

Biochemistry (1989)

NMR Based Docking Studies of Lac Repressor Headpiece on a Lac Operator Fragment

Ucla Symp.Mol.Cell.Biol., New Ser. (1989)

The Interaction of Lac Repressor Headpiece with its Operator: An NMR View

Protein Seq.Data Anal. (1988)

;Combined Procedure of Distance Geometry and Restrained Molecular Dynamics Techniques for Protein Structure Determination from Nuclear Magnetic Resonance Data: Application to the DNA Binding Domain of Lac Repressor from Escherichia Coli ;

Proteins (1988)

A Two-Dimensional NMR Study of the Complex of Lac Repressor Headpiece with a 14 Base Pair Lac Operator Fragment

Nato Asi Ser.,Ser.A (1987)

Complex of Lac Repressor Headpiece with a 14 Base Pair Lac Operator Fragment Studied by Two-Dimensional Nuclear Magnetic Resonance

J.Mol.Biol. (1987)

;Restrained Molecular Dynamics Procedure for Protein Tertiary Structure Determination from NMR Data: A Lac Repressor Headpiece Structure Based on Information on J-Coupling and from Presence and Absence of Noes ;

Isr.J.Chem. (1986)

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晶胞边长 a length_a	1.000 Å
晶胞边长 b length_b	1.000 Å
晶胞边长 c length_c	1.000 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	1

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

fit	/app/data/saxs_computation/lc/1lcd/1lcd.fit
pddf	/app/data/pr_computation/lc/1lcd/1lcd.pr.out
profile	/app/data/saxs_computation/lc/1lcd/1lcd.dat

;STRUCTURE OF THE COMPLEX OF LAC REPRESSOR HEADPIECE AND AN 11 BASE-PAIR HALF-OPERATOR DETERMINED BY NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY AND RESTRAINED MOLECULAR DYNAMICS ;

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

5. 实体与聚合体信息 (5)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

Entity 3 polymer

聚合体 Polymer

来源 Source

Entity 4 non-polymer

Entity 5 water

6. 折叠分类 (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. 引用文献 (10)

8. 文件与曲线 (10)

Files (7)

Curves (3)