SAXSdb — 1mey

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1mey
沉积日期 deposition_date	1996-09-27
结构标题 title	CRYSTAL STRUCTURE OF A DESIGNED ZINC FINGER PROTEIN BOUND TO DNA
关键词 keywords	ZINC FINGER, PROTEIN-DNA INTERACTION, PROTEIN DESIGN, COMPLEX (ZINC FINGER-DNA), TRANSFERASE-DNA COMPLEX; TRANSFERASE/DNA
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	26.92 Å
回转半径 Rg (电子) rg_electron	27.16 Å
零角强度 I(0) i0	46190400.00
分子量 molecular_weight	39227.0 kDa
排除体积 excluded_volume	42954 Å³
包络体积 envelope_volume	58793 Å³
水化壳体积 shell_volume	19815 Å³
包络直径 envelope_diameter	89.3 Å
壳层 Rg shell_rg	31.60 Å
包络 Rg envelope_rg	27.07 Å
形状 Rg shape_rg	27.12 Å
总 Rg total_rg	27.60 Å
总原子数 total_atoms	2641
残基数 n_residues	245
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	86.9 Å
Rg (实空间) rg_real	27.22 Å
Rg 误差 (实空间) rg_real_error	0.71 Å
I(0) (实空间) i0_real	4.6190e+07
I(0) 误差 (实空间) i0_real_error	6.0230e+05
Rg (倒空间) rg_reciprocal	27.13 Å
I(0) (倒空间) i0_reciprocal	46190000.0000
解质量估计 total_estimate	0.8244
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	22.1 Å
偏度 Skewness skewness	0.471
峰度 Kurtosis kurtosis	-0.606
角度范围 angular_range	— – 0.2950 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	3411000.0000
实空间数据点数 n_real_points	60
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.803; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.562; Smooth: 0.743

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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	;DNA (5'-D(APTPGPAPGPGPCPAPGPAPAPCP*T)-3') ;
分子量 formula_weight	4024.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polydeoxyribonucleotide
链编号 strand_id	A,D
原子数 atom_count	2773

ATGAGGCAGAACT

Entity 2 polymer

描述 description	;DNA (5'-D(TPAPGPTPTPCPTPGPCPCPTP(C38)P*A)-3') ;
分子量 formula_weight	4043.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polydeoxyribonucleotide
链编号 strand_id	B,E

TAGTTCTGCCTCA

Entity 3 polymer

描述 description	CONSENSUS ZINC FINGER
分子量 formula_weight	10147.4 kDa
来源方法 src_method	man
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	C,F,G

MEKPYKCPECGKSFSQSSNLQKHQRTHTGEKPYKCPECGKSFSQSSDLQKHQRTHTGEKPYKCPECGKSFSRSDHLSRHQRTHQNKK

来源 Source

宿主生物 host_organism

Escherichia coli BL21(DE3)

Entity 4 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	8

Entity 5 non-polymer

描述 description	CHLORIDE ION
分子量 formula_weight	35.5 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	132

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6. 折叠分类 (SCOP + CATH) 9 domains

SCOP 2.08 (3 domains)

结构域编号 domain_id	d1meyc_
类 Class class	k — Designed proteins
折叠类型 Fold fold	k.12 — Zinc finger design
超家族 Superfamily superfamily	k.12.1 — Zinc finger design
家族 Family family	k.12.1.1 — Zinc finger design

结构域编号 domain_id	d1meyf_
类 Class class	k — Designed proteins
折叠类型 Fold fold	k.12 — Zinc finger design
超家族 Superfamily superfamily	k.12.1 — Zinc finger design
家族 Family family	k.12.1.1 — Zinc finger design

结构域编号 domain_id	d1meyg_
类 Class class	k — Designed proteins
折叠类型 Fold fold	k.12 — Zinc finger design
超家族 Superfamily superfamily	k.12.1 — Zinc finger design
家族 Family family	k.12.1.1 — Zinc finger design

CATH v4.4 (6 domains)

结构域编号 domain_id	1meyC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	160 — Double Stranded RNA Binding Domain
同源超家族 H-superfamily homologous superfamily	60 — Classic Zinc Finger

结构域编号 domain_id	1meyC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	160 — Double Stranded RNA Binding Domain
同源超家族 H-superfamily homologous superfamily	60 — Classic Zinc Finger

结构域编号 domain_id	1meyC03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	160 — Double Stranded RNA Binding Domain
同源超家族 H-superfamily homologous superfamily	60 — Classic Zinc Finger

结构域编号 domain_id	1meyF01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	160 — Double Stranded RNA Binding Domain
同源超家族 H-superfamily homologous superfamily	60 — Classic Zinc Finger

结构域编号 domain_id	1meyF02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	160 — Double Stranded RNA Binding Domain
同源超家族 H-superfamily homologous superfamily	60 — Classic Zinc Finger

结构域编号 domain_id	1meyF03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	160 — Double Stranded RNA Binding Domain
同源超家族 H-superfamily homologous superfamily	60 — Classic Zinc Finger

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7. 引用文献 (5)

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晶胞边长 a length_a	62.070 Å
晶胞边长 b length_b	165.530 Å
晶胞边长 c length_c	46.274 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	12

空间群 space_group	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	2.200 Å
最低分辨率 resolution_low	6.000 Å
R 因子 r_factor	0.2240
R_work r_work	0.2240
R_free r_free	0.3190

fit	/app/data/saxs_computation/me/1mey/1mey.fit
pddf	/app/data/pr_computation/me/1mey/1mey.pr.out
profile	/app/data/saxs_computation/me/1mey/1mey.dat

CRYSTAL STRUCTURE OF A DESIGNED ZINC FINGER PROTEIN BOUND TO DNA

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

5. 实体与聚合体信息 (6)

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 non-polymer

Entity 6 water

6. 折叠分类 (SCOP + CATH) 9 domains

SCOP 2.08 (3 domains)

CATH v4.4 (6 domains)

7. 引用文献 (5)

8. 文件与曲线 (10)

Files (7)

Curves (3)