SAXSdb — 1pa6

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1pa6
沉积日期 deposition_date	2003-05-13
结构标题 title	Crystal structure of the OXYTRICHA nova telomere end-binding protein complexed with noncognate ssDNA GGGGTTTTGAGG
关键词 keywords	;SINGLE STRAND DNA BINDING PROTEIN, PROTEIN DNA INTERACTIONS, SEQUENCE SPECIFICITY, NONCOGNATE, OLIGONUCLEOTIDE AND OLIGOSACCHARIDE BINDING FOLD, OB FOLD, TELOMERES, PROTEIN/DNA, DNA BINDING PROTEIN-DNA COMPLEX ;; DNA BINDING PROTEIN/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	31.91 Å
回转半径 Rg (电子) rg_electron	30.71 Å
零角强度 I(0) i0	140348000.00
分子量 molecular_weight	88359.0 kDa
排除体积 excluded_volume	108020 Å³
包络体积 envelope_volume	138090 Å³
水化壳体积 shell_volume	38122 Å³
包络直径 envelope_diameter	111.8 Å
壳层 Rg shell_rg	37.19 Å
包络 Rg envelope_rg	30.62 Å
形状 Rg shape_rg	30.63 Å
总 Rg total_rg	31.49 Å
总原子数 total_atoms	6202
残基数 n_residues	712
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	106.0 Å
Rg (实空间) rg_real	31.93 Å
Rg 误差 (实空间) rg_real_error	0.90 Å
I(0) (实空间) i0_real	1.4030e+08
I(0) 误差 (实空间) i0_real_error	2.1340e+06
Rg (倒空间) rg_reciprocal	31.92 Å
I(0) (倒空间) i0_reciprocal	140300000.0000
解质量估计 total_estimate	0.8848
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	36.0 Å
偏度 Skewness skewness	0.329
峰度 Kurtosis kurtosis	-0.338
角度范围 angular_range	— – 0.2500 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	13970000.0000
实空间数据点数 n_real_points	51
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.890; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.835

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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 (7)

Entity 1 polymer

描述 description	5'-D(GPGPGPGPTPTPTPTPGPAPGPG)-3'
分子量 formula_weight	3789.5 kDa
突变 mutation	G10A
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	D
原子数 atom_count	6705

GGGGTTTTGAGG

Entity 2 polymer

描述 description	5'-D(GPGPGPGPTPTPTPTPGPGPGPG)-3'
分子量 formula_weight	3805.5 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	G,H

GGGGTTTTGGGG

Entity 3 polymer

描述 description	Telomere-binding protein alpha subunit
分子量 formula_weight	52460.0 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

YEYVELAKASLTSAQPQHFYAVVIDATFPYKTNQERYICSLKIVDPTLYLKQQKGAGDASDYATLVLYAKRFEDLPIIHRAGDIIRVHRATLRLYNGQRQFNANVFYSSSWALFSTDKRSVTQEINNQDAVSDTTPFSFSSKHATIEKNEISILQNLRKWANQYFSSYSVISSDMYTALNKAQAQKGDFDVVAKILQVHELDEYTNELKLKDASGQVFYTLSLKLKFPHVRTGEVVRIRSATYDETSTQKKVLILSHYSNIITFIQSSKLAKELRAKIQDDHSVEVASLKKNVSLNAVVLTEVDKKHAALPSTSLQDLFHHADSDKELQAQDTFRTQFYVTKIEPSDVKEWVKGYDRKTKKSSSLKGASGKGDNIFQVQFLVKDASTQLNNNTYRVLLYTQDGLGANFFNVKADNLHKNADARKKLEDSAELLTKFNSYVDAVVERRNGFYLIKDTKLIY

来源 Source

来源生物 organism	Sterkiella nova
NCBI 分类编号 ncbi_taxonomy_id	200597
宿主生物 host_organism	Escherichia coli

Entity 4 polymer

描述 description	Telomere-binding protein beta subunit
分子量 formula_weight	24487.7 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	B

QQQSAFKQLYTELFNNEGDFSKVSSNLKKPLKCYVKESYPHFLVTDGYFFVAPYFTKEAVNEFHAKFPNVNIVDLTDKVIVINNWSLELRRVNSAEVFTSYANLEARLIVHSFKPNLQERLNPTRYPVNLFRDDEFKTTIQHFRHTALQAAINKTVKGDNLVDISKVADAAGKKGKVDAGIVKASASKGDEFSDFSFKEGNTATLKIADIFVQEKG

来源 Source

来源生物 organism	Sterkiella nova
NCBI 分类编号 ncbi_taxonomy_id	200597
宿主生物 host_organism	Escherichia coli

Entity 5 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	4

Entity 6 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 7 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	503

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6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1pa6a1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.40 — OB-fold
超家族 Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
家族 Family family	b.40.4.3 — Single strand DNA-binding domain, SSB

结构域编号 domain_id	d1pa6a2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.40 — OB-fold
超家族 Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
家族 Family family	b.40.4.3 — Single strand DNA-binding domain, SSB

结构域编号 domain_id	d1pa6a3
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.40 — OB-fold
超家族 Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
家族 Family family	b.40.4.3 — Single strand DNA-binding domain, SSB

结构域编号 domain_id	d1pa6b_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.40 — OB-fold
超家族 Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
家族 Family family	b.40.4.3 — Single strand DNA-binding domain, SSB

CATH v4.4 (4 domains)

结构域编号 domain_id	1pa6A01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
同源超家族 H-superfamily homologous superfamily	140 — Nucleic acid-binding proteins

结构域编号 domain_id	1pa6A02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
同源超家族 H-superfamily homologous superfamily	140 — Nucleic acid-binding proteins

结构域编号 domain_id	1pa6A03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
同源超家族 H-superfamily homologous superfamily	140 — Nucleic acid-binding proteins

结构域编号 domain_id	1pa6B00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	200 — Telomere-binding Protein Beta Subunit; Chain B
同源超家族 H-superfamily homologous superfamily	10 — Telomere-binding Protein Beta Subunit; Chain

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7. 引用文献 (1)

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晶胞边长 a length_a	93.110 Å
晶胞边长 b length_b	93.110 Å
晶胞边长 c length_c	422.680 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	120.00 °
晶胞分子数 Z z_pdb	24

空间群 space_group	P 61 2 2
空间群编号 int_tables_number	178
晶系 crystal_system	—

分辨率 resolution	2.450 Å
最低分辨率 resolution_low	29.790 Å
R 因子 r_factor	0.2640
R_work r_work	0.2230
R_free r_free	0.2680

fit	/app/data/saxs_computation/pa/1pa6/1pa6.fit
pddf	/app/data/pr_computation/pa/1pa6/1pa6.pr.out
profile	/app/data/saxs_computation/pa/1pa6/1pa6.dat

Crystal structure of the OXYTRICHA nova telomere end-binding protein complexed with noncognate ssDNA GGGGTTTTGAGG

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 (7)

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 polymer

聚合体 Polymer

来源 Source

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 water

6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)