SAXSdb — 1gu5

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1gu5
沉积日期 deposition_date	2002-01-24
结构标题 title	Crystal structure of C/EBPBETA BZIP homodimer bound to a DNA fragment from the MIM-1 promoter
关键词 keywords	TRANSCRIPTION/DNA, PROTEIN-DNA COMPLEX, TRANSCRIPTION FACTOR, BZIP, C/EBP, TRANSCRIPTION-DNA complex; 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	25.78 Å
回转半径 Rg (电子) rg_electron	27.72 Å
零角强度 I(0) i0	18427300.00
分子量 molecular_weight	25880.0 kDa
排除体积 excluded_volume	29439 Å³
包络体积 envelope_volume	41414 Å³
水化壳体积 shell_volume	15074 Å³
包络直径 envelope_diameter	100.9 Å
壳层 Rg shell_rg	29.20 Å
包络 Rg envelope_rg	28.27 Å
形状 Rg shape_rg	27.80 Å
总 Rg total_rg	27.70 Å
总原子数 total_atoms	1779
残基数 n_residues	166
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	98.3 Å
Rg (实空间) rg_real	26.41 Å
Rg 误差 (实空间) rg_real_error	1.31 Å
I(0) (实空间) i0_real	1.8430e+07
I(0) 误差 (实空间) i0_real_error	2.9030e+05
Rg (倒空间) rg_reciprocal	26.22 Å
I(0) (倒空间) i0_reciprocal	18420000.0000
解质量估计 total_estimate	0.6866
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	19.0 Å
偏度 Skewness skewness	0.776
峰度 Kurtosis kurtosis	-0.075
角度范围 angular_range	— – 0.3100 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	1295000.0000
实空间数据点数 n_real_points	63
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.295; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.090; Smooth: 0.946

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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	CAAT/ENHANCER BINDING PROTEIN BETA
分子量 formula_weight	9381.9 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
原子数 atom_count	2003

VKSKAKKTVDKHSDEYKIRRERNNIAVRKSRDKAKMRNLETQHKVLELTAENERLQKKVEQLSRELSTLRNLFKQLPE

来源 Source

来源生物 organism	HOMO SAPIENS
通用名 common_name	HUMAN
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 polymer

描述 description	;5'-D(TPTPGPTPGPTPTPGPGPCP* CPAPAPTPCP*A)-3' ;
分子量 formula_weight	4904.2 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

TTGTGTTGGCCAATCA

Entity 3 polymer

描述 description	;5'-D(APTPGPAPTPTPGPGPCPCP* APAPCPAPCP*A)-3' ;
分子量 formula_weight	4891.2 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	D

ATGATTGGCCAACACA

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	224

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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	d1gu5a_
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	d1gu5b_
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	1gu5A00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	170 —

结构域编号 domain_id	1gu5B00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	170 —

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7. 引用文献 (6)

Structural Basis for Flexible Base Recognition by C/Ebpbeta

To be Published

PRIMARY

Mechanism of C-Myb-C/Ebpbeta Cooperation from Separated Sites on a Promoter

Cell (Cambridge,Mass.) (2002)

PMID: 11792321 · DOI: 10.1016/S0092-8674(01)00636-5

Crystallization and Preliminary X-Ray Analysis of the C/Ebpbeta C-Terminal Region in Complex with DNA

Acta Crystallogr.,Sect.D (2001)

PMID: 11375506 · DOI: 10.1107/S0907444901003912

Structural Analyses of DNA Recognition by the Aml1/ Runx-1 Runt Domain and its Allosteric Control by Cbfbeta

Cell (Cambridge,Mass.) (2001)

PMID: 11257229 · DOI: 10.1016/S0092-8674(01)00271-9

;Crystallization and Preliminary X-Ray Analyses of Quaternary, Ternary and Binary Protein-DNA Complexes with Involvement of Aml1/Runx-1/Cbfalpha Runt Domain, Cbfbeta and the C/Ebpbeta bZIP Region ;

Acta Crystallogr.,Sect.D (2001)

PMID: 11375505 · DOI: 10.1107/S0907444901003900

;Crystals of Ternary Protein-DNA Complexes Composed of DNA-Binding Domains C-Myb or V-Myb, C/Ebpalpha or C/Ebpbeta and Tom-1A Promoter Fragment ;

Acta Crystallogr.,Sect.D (2001)

PMID: 11679735 · DOI: 10.1107/S0907444901011982

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晶胞边长 a length_a	101.596 Å
晶胞边长 b length_b	113.037 Å
晶胞边长 c length_c	74.498 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	C 2 2 21
空间群编号 int_tables_number	20
晶系 crystal_system	—

分辨率 resolution	2.100 Å
最低分辨率 resolution_low	29.740 Å
R 因子 r_factor	0.2290
R_work r_work	0.2290
R_free r_free	0.2770

fit	/app/data/saxs_computation/gu/1gu5/1gu5.fit
pddf	/app/data/pr_computation/gu/1gu5/1gu5.pr.out
profile	/app/data/saxs_computation/gu/1gu5/1gu5.dat

Crystal structure of C/EBPBETA BZIP homodimer bound to a DNA fragment from the MIM-1 promoter

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

衍射实验 Diffraction

5. 实体与聚合体信息 (4)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

Entity 3 polymer

聚合体 Polymer

Entity 4 water

6. 折叠分类 (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. 引用文献 (6)

8. 文件与曲线 (10)

Files (7)

Curves (3)