1pyi

CRYSTAL STRUCTURE OF A PPR1-DNA COMPLEX: DNA RECOGNITION BY PROTEINS CONTAINING A ZN2CYS6 BINUCLEAR CLUSTER

Method: X-RAY DIFFRACTION D_max: 69.2 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	1pyi
沉积日期 deposition_date	1995-01-04
结构标题 title	CRYSTAL STRUCTURE OF A PPR1-DNA COMPLEX: DNA RECOGNITION BY PROTEINS CONTAINING A ZN2CYS6 BINUCLEAR CLUSTER
关键词 keywords	PROTEIN-DNA COMPLEX, TRANSCRIPTION-DNA COMPLEX, GAL4, ZINC FINGER, ZN2CYS6, BINUCLEAR CLUSTER, TRANSCRIPTION FACTOR; TRANSCRIPTION/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	20.94 Å
回转半径 Rg (电子) rg_electron	20.44 Å
零角强度 I(0) i0	18698300.00
分子量 molecular_weight	26844.0 kDa
排除体积 excluded_volume	31024 Å³
包络体积 envelope_volume	39294 Å³
水化壳体积 shell_volume	17102 Å³
包络直径 envelope_diameter	68.5 Å
壳层 Rg shell_rg	25.60 Å
包络 Rg envelope_rg	20.42 Å
形状 Rg shape_rg	20.44 Å
总 Rg total_rg	21.05 Å
总原子数 total_atoms	1825
残基数 n_residues	186
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	69.2 Å
Rg (实空间) rg_real	20.99 Å
Rg 误差 (实空间) rg_real_error	0.45 Å
I(0) (实空间) i0_real	1.8700e+07
I(0) 误差 (实空间) i0_real_error	2.4630e+05
Rg (倒空间) rg_reciprocal	20.98 Å
I(0) (倒空间) i0_reciprocal	18700000.0000
解质量估计 total_estimate	0.8981
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	23.1 Å
偏度 Skewness skewness	0.347
峰度 Kurtosis kurtosis	-0.404
角度范围 angular_range	— – 0.3800 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	1354000.0000
实空间数据点数 n_real_points	70
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.919; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.933; Smooth: 0.980

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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 (4)

Entity 1 polymer

描述 description	;DNA (5'-D(TPCPGPGPCPAPAPTPTPGPCPCPGPA)-3') ;
分子量 formula_weight	4280.8 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	D,E
原子数 atom_count	1826

TCGGCAATTGCCGA

Entity 2 polymer

描述 description	PROTEIN (PYRIMIDINE PATHWAY REGULATOR 1)
分子量 formula_weight	10956.9 kDa
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

MKSRTACKRCRLKKIKCDQEFPSCKRCAKLEVPCVSLDPATGKDVPRSYVFFLEDRLAVMMRVLKEYGVDPTKIRGNIPATSDDEPFDLKKYSSVS

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
宿主生物 host_organism	Escherichia coli

Entity 3 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 4 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	1

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6. 折叠分类 (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1pyia1
类 Class class	g — Small proteins
折叠类型 Fold fold	g.38 — Zn2/Cys6 DNA-binding domain
超家族 Superfamily superfamily	g.38.1 — Zn2/Cys6 DNA-binding domain
家族 Family family	g.38.1.1 — Zn2/Cys6 DNA-binding domain

结构域编号 domain_id	d1pyia2
类 Class class	h — Coiled coil proteins
折叠类型 Fold fold	h.1 — Parallel coiled-coil
超家族 Superfamily superfamily	h.1.3 — Leucine zipper domain
家族 Family family	h.1.3.1 — Leucine zipper domain

结构域编号 domain_id	d1pyib1
类 Class class	g — Small proteins
折叠类型 Fold fold	g.38 — Zn2/Cys6 DNA-binding domain
超家族 Superfamily superfamily	g.38.1 — Zn2/Cys6 DNA-binding domain
家族 Family family	g.38.1.1 — Zn2/Cys6 DNA-binding domain

结构域编号 domain_id	d1pyib2
类 Class class	h — Coiled coil proteins
折叠类型 Fold fold	h.1 — Parallel coiled-coil
超家族 Superfamily superfamily	h.1.3 — Leucine zipper domain
家族 Family family	h.1.3.1 — Leucine zipper domain

CATH v4.4 (2 domains)

结构域编号 domain_id	1pyiA01
类 Class class	4 — Few Secondary Structures
架构 Architecture architecture	10 — Irregular
拓扑 Topology topology	240 — CD2-Gal4
同源超家族 H-superfamily homologous superfamily	10 — Zn(2)-C6 fungal-type DNA-binding domain

结构域编号 domain_id	1pyiB00
类 Class class	4 — Few Secondary Structures
架构 Architecture architecture	10 — Irregular
拓扑 Topology topology	240 — CD2-Gal4
同源超家族 H-superfamily homologous superfamily	10 — Zn(2)-C6 fungal-type DNA-binding domain

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7. 引用文献 (2)

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晶胞边长 a length_a	53.800 Å
晶胞边长 b length_b	92.600 Å
晶胞边长 c length_c	174.700 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	16

空间群 space_group	I 2 2 2
空间群编号 int_tables_number	23
晶系 crystal_system	—

分辨率 resolution	3.200 Å
最低分辨率 resolution_low	10.000 Å
R 因子 r_factor	0.2450
R_work r_work	—
R_free r_free	0.3300

fit	/app/data/saxs_computation/py/1pyi/1pyi.fit
pddf	/app/data/pr_computation/py/1pyi/1pyi.pr.out
profile	/app/data/saxs_computation/py/1pyi/1pyi.dat

CRYSTAL STRUCTURE OF A PPR1-DNA COMPLEX: DNA RECOGNITION BY PROTEINS CONTAINING A ZN2CYS6 BINUCLEAR CLUSTER

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 (4)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 non-polymer

Entity 4 water

6. 折叠分类 (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

7. 引用文献 (2)

8. 文件与曲线 (10)

Files (7)

Curves (3)