1p7h

Structure of NFAT1 bound as a dimer to the HIV-1 LTR kB element

Method: X-RAY DIFFRACTION D_max: 125.8 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	1p7h
沉积日期 deposition_date	2003-05-01
结构标题 title	Structure of NFAT1 bound as a dimer to the HIV-1 LTR kB element
关键词 keywords	DNA Binding protein, Transcription regulation, Activator, 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	38.71 Å
回转半径 Rg (电子) rg_electron	39.02 Å
零角强度 I(0) i0	390460000.00
分子量 molecular_weight	145960.0 kDa
排除体积 excluded_volume	176680 Å³
包络体积 envelope_volume	255440 Å³
水化壳体积 shell_volume	54738 Å³
包络直径 envelope_diameter	129.9 Å
壳层 Rg shell_rg	44.56 Å
包络 Rg envelope_rg	38.17 Å
形状 Rg shape_rg	39.03 Å
总 Rg total_rg	39.30 Å
总原子数 total_atoms	10206
残基数 n_residues	1204
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	125.8 Å
Rg (实空间) rg_real	38.56 Å
Rg 误差 (实空间) rg_real_error	0.86 Å
I(0) (实空间) i0_real	3.9050e+08
I(0) 误差 (实空间) i0_real_error	5.7640e+06
Rg (倒空间) rg_reciprocal	38.66 Å
I(0) (倒空间) i0_reciprocal	390500000.0000
解质量估计 total_estimate	0.8991
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	49.1 Å
偏度 Skewness skewness	0.165
峰度 Kurtosis kurtosis	-0.492
角度范围 angular_range	— – 0.2050 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	30280000.0000
实空间数据点数 n_real_points	42
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.913; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.947

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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	5'-D(APAPTPGPGPGPGPAPCPTPTPTPCPCP*A)-3'
分子量 formula_weight	4609.0 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,C
原子数 atom_count	10395

AATGGGGACTTTCCA

Entity 2 polymer

描述 description	5'-D(TPTPTPGPGPAPAPAPGPTPCPCPCPCP*A)-3'
分子量 formula_weight	4569.0 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,D

TTTGGAAAGTCCCCA

Entity 3 polymer

描述 description	Nuclear factor of activated T-cells, cytoplasmic 2
分子量 formula_weight	32487.0 kDa
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	L,M,N,O

SSVPLEWPLSSQSGSYELRIEVQPKPHHRAHYETEGSRGAVKAPTGGHPVVQLHGYMENKPLGLQIFIGTADERILKPHAFYQVHRITGKTVTTTSYEKIVGNTKVLEIPLEPKNNMRATIDCAGILKLRNADIELRKGETDIGRKNTRVRLVFRVHIPESSGRIVSLQTASNPIECSQRSAHELPMVERQDTDSCLVYGGQQMILTGQNFTSESKVVFTEKTTDGQQIWEMEATVDKDKSQPNMLFVEIPEYRNKHIRTPVKVNFYVINGKRKRSQPQHFTYHPV

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

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	189

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6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d1p7hl1
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	d1p7hl2
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	d1p7hm1
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	d1p7hm2
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	d1p7hn1
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	d1p7hn2
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	d1p7ho1
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	d1p7ho2
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 (8 domains)

结构域编号 domain_id	1p7hL01
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	1p7hL02
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	1p7hM01
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	1p7hM02
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	1p7hN01
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	1p7hN02
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	1p7hO01
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	1p7hO02
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	74.107 Å
晶胞边长 b length_b	80.321 Å
晶胞边长 c length_c	80.308 Å
晶胞夹角 α angle_alpha	71.20 °
晶胞夹角 β angle_beta	78.97 °
晶胞夹角 γ angle_gamma	78.94 °
晶胞分子数 Z z_pdb	4

空间群 space_group	P 1
空间群编号 int_tables_number	1
晶系 crystal_system	—

分辨率 resolution	2.600 Å
最低分辨率 resolution_low	29.680 Å
R 因子 r_factor	0.2310
R_work r_work	0.2310
R_free r_free	0.2650

fit	/app/data/saxs_computation/p7/1p7h/1p7h.fit
pddf	/app/data/pr_computation/p7/1p7h/1p7h.pr.out
profile	/app/data/saxs_computation/p7/1p7h/1p7h.dat

Structure of NFAT1 bound as a dimer to the HIV-1 LTR kB element

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

Entity 3 polymer

聚合体 Polymer

来源 Source

Entity 4 water

6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)