SAXSdb — 1nfk

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1nfk
沉积日期 deposition_date	1995-02-28
结构标题 title	STRUCTURE OF THE NUCLEAR FACTOR KAPPA-B (NF-KB) P50 HOMODIMER
关键词 keywords	NF-KB P50, COMPLEX (TRANSCRIPTION FACTOR-DNA), 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	31.47 Å
回转半径 Rg (电子) rg_electron	31.87 Å
零角强度 I(0) i0	102944000.00
分子量 molecular_weight	76405.0 kDa
排除体积 excluded_volume	93915 Å³
包络体积 envelope_volume	122650 Å³
水化壳体积 shell_volume	33556 Å³
包络直径 envelope_diameter	107.6 Å
壳层 Rg shell_rg	36.87 Å
包络 Rg envelope_rg	31.98 Å
形状 Rg shape_rg	31.90 Å
总 Rg total_rg	32.18 Å
总原子数 total_atoms	6526
残基数 n_residues	646
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	104.5 Å
Rg (实空间) rg_real	31.52 Å
Rg 误差 (实空间) rg_real_error	1.14 Å
I(0) (实空间) i0_real	1.0290e+08
I(0) 误差 (实空间) i0_real_error	1.6060e+06
Rg (倒空间) rg_reciprocal	31.50 Å
I(0) (倒空间) i0_reciprocal	102900000.0000
解质量估计 total_estimate	0.8920
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	0
主峰位置 r_peak_primary	— Å
偏度 Skewness skewness	0.339
峰度 Kurtosis kurtosis	-0.456
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	16630000.0000
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: 0.903; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.970; Smooth: 0.913

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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 (3)

Entity 1 polymer

描述 description	;DNA (5'-D(TPGPGPGPAPAPTPTPCPCP*C)-3') ;
分子量 formula_weight	3349.2 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	C,D
原子数 atom_count	7477

TGGGAATTCCC

Entity 2 polymer

描述 description	PROTEIN (NUCLEAR FACTOR KAPPA-B (NF-KB))
分子量 formula_weight	36597.8 kDa
来源方法 src_method	nat
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

GPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGVCTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHSDLAYLQAEGGGDRQLTDREKEIIRQAAVQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDVNITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQK

Entity 3 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	317

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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	d1nfka1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.18 — E set domains
家族 Family family	b.1.18.1 — NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain

结构域编号 domain_id	d1nfka2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.2 — Common fold of diphtheria toxin/transcription factors/cytochrome f
超家族 Superfamily superfamily	b.2.5 — p53-like transcription factors
家族 Family family	b.2.5.3 — Rel/Dorsal transcription factors, DNA-binding domain

结构域编号 domain_id	d1nfkb1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.18 — E set domains
家族 Family family	b.1.18.1 — NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain

结构域编号 domain_id	d1nfkb2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.2 — Common fold of diphtheria toxin/transcription factors/cytochrome f
超家族 Superfamily superfamily	b.2.5 — p53-like transcription factors
家族 Family family	b.2.5.3 — Rel/Dorsal transcription factors, DNA-binding domain

CATH v4.4 (4 domains)

结构域编号 domain_id	1nfkA01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	340 — Rel homology domain (RHD), DNA-binding domain

结构域编号 domain_id	1nfkA02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

结构域编号 domain_id	1nfkB01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	340 — Rel homology domain (RHD), DNA-binding domain

结构域编号 domain_id	1nfkB02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

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7. 引用文献 (1)

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晶胞边长 a length_a	84.200 Å
晶胞边长 b length_b	132.100 Å
晶胞边长 c length_c	80.100 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	93.10 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	—

分辨率 resolution	2.300 Å
最低分辨率 resolution_low	6.000 Å
R 因子 r_factor	0.2300
R_work r_work	0.2300
R_free r_free	0.3400

fit	/app/data/saxs_computation/nf/1nfk/1nfk.fit
pddf	/app/data/pr_computation/nf/1nfk/1nfk.pr.out
profile	/app/data/saxs_computation/nf/1nfk/1nfk.dat

STRUCTURE OF THE NUCLEAR FACTOR KAPPA-B (NF-KB) P50 HOMODIMER

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 (3)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

Entity 3 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)