1ny6

Crystal structure of sigm54 activator (AAA+ ATPase) in the active state

Method: X-RAY DIFFRACTION Dmax: 165.0 Å Quality: GOOD

1. 蛋白身份与相关结构 Protein Identity & Related Structures

transcriptional regulator (NtrC family)

Aquifex aeolicus

UniProt O67198

当前结构中的状态

Assembly 聚集状态 构建体 突变与修饰 配体、离子与共同组分 实验方法与环境 结构质量
1 蛋白同源多聚体 同源多聚体 蛋白 × 7 PDB 声明:heptameric(7) 与蛋白拷贝数一致 链 A; UniProt 122–387 链 B; UniProt 122–387 链 C; UniProt 122–387 链 D; UniProt 122–387 链 E; UniProt 122–387 链 F; UniProt 122–387 链 G; UniProt 122–387 片段:residues 122-387 ADP ADENOSINE-5'-DIPHOSPHATE × 7 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;pH 6.5;298 K;diammonium tartrate, PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K 分辨率 3.10 Å R-free 0.329
2 蛋白同源多聚体 同源多聚体 蛋白 × 7 PDB 声明:heptameric(7) 与蛋白拷贝数一致 链 H; UniProt 122–387 链 I; UniProt 122–387 链 J; UniProt 122–387 链 K; UniProt 122–387 链 L; UniProt 122–387 链 M; UniProt 122–387 链 N; UniProt 122–387 片段:residues 122-387 ADP ADENOSINE-5'-DIPHOSPHATE × 7 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;pH 6.5;298 K;diammonium tartrate, PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K 分辨率 3.10 Å R-free 0.329

数据库中的同蛋白其他状态

以下每一行都是同一 UniProt 蛋白在另一个 PDB 条目中的 biological assembly, “相对当前条目”直接指出证据层面的不同;没有差异标签表示当前已读取字段一致。

共 12 个其他 PDB 条目、22 个 assembly。 打开独立比较页并筛选聚集状态

查看构建体与数据证据
UniProt名称 O67198_AQUAE
Isoform
PDB实体 1
链与序列区间 作者链 A; PDB构建体 1–267; UniProt 122–387 作者链 B; PDB构建体 1–267; UniProt 122–387 作者链 C; PDB构建体 1–267; UniProt 122–387 作者链 D; PDB构建体 1–267; UniProt 122–387 作者链 E; PDB构建体 1–267; UniProt 122–387 作者链 F; PDB构建体 1–267; UniProt 122–387 作者链 G; PDB构建体 1–267; UniProt 122–387 作者链 H; PDB构建体 1–267; UniProt 122–387 作者链 I; PDB构建体 1–267; UniProt 122–387 作者链 J; PDB构建体 1–267; UniProt 122–387 作者链 K; PDB构建体 1–267; UniProt 122–387 作者链 L; PDB构建体 1–267; UniProt 122–387 作者链 M; PDB构建体 1–267; UniProt 122–387 作者链 N; PDB构建体 1–267; UniProt 122–387

页面优先展示蛋白身份、当前 assembly、共同组分、聚集状态和跨 PDB 结构链接。 链映射与序列区间收在“数据证据”中;数据库内部编号、导入时间和 assembly 操作表达式仅用于维护,因此不在读者页面展示。

SAXS 散射曲线 SAXS Profile

SAXS profile for 1ny6

P(r) 距离分布 P(r) Distribution

P(r) distribution for 1ny6
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2. 结构基本信息 2. Structure Basics

条目编号 entry_id1ny6
沉积日期 deposition_date2003-02-11
结构标题 titleCrystal structure of sigm54 activator (AAA+ ATPase) in the active state
关键词 keywordsAAA+ ATPase, sigma54 activator, bacterial transcription, heptamer, TRANSCRIPTION; TRANSCRIPTION
实验方法 methodX-RAY DIFFRACTION

3. SAXS 参数 (CRYSOL 理论计算) 3. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier51.14
回转半径 Rg (电子) rg_electron50.74
零角强度 I(0) i02094170000.00
分子量 molecular_weight397740.0 kDa
排除体积 excluded_volume504920 ų
包络体积 envelope_volume729420 ų
水化壳体积 shell_volume117870 ų
包络直径 envelope_diameter174.8
壳层 Rg shell_rg57.44
包络 Rg envelope_rg48.35
形状 Rg shape_rg50.72
总 Rg total_rg51.06
总原子数 total_atoms28041
残基数 n_residues3456
球谐函数阶数 n_harmonics20
q 范围 q_range— – 0.5000 −1
数据点数 n_points101
壳层类型 shell_typedirectional
溶剂电子密度 solvent_density0.3340 e/ų
壳层衬度 contrast_shell0.0300 e/ų
CRYSOL 版本 crysol_version4.1.3

4. P(r) 距离分布 (GNOM 反演) 4. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax165.0
Rg (实空间) rg_real50.95
Rg 误差 (实空间) rg_real_error1.38
I(0) (实空间) i0_real2.0940e+09
I(0) 误差 (实空间) i0_real_error3.7810e+07
Rg (倒空间) rg_reciprocal51.30
I(0) (倒空间) i0_reciprocal2095000000.0000
解质量估计 total_estimate0.8719
解质量评级 solution_quality GOOD a GOOD solution
P(r) 峰数 n_peaks2
主峰位置 r_peak_primary63.9
偏度 Skewness skewness0.169
峰度 Kurtosis kurtosis-0.340
角度范围 angular_range— – 0.1550 −1
当前正则化参数 α current_alpha0.0000
最高正则化参数 α highest_alpha170200000.0000
实空间数据点数 n_real_points32
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.000; Oscil: 0.844; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.978; Smooth: 0.823

5. 晶体学与实验 5. Crystallography & Experiment

6. 实体与聚合物信息 Entities & Polymers (2)

7. 折叠分类 (SCOP + CATH) 42 domains

SCOP 2.08 (14 domains)

结构域编号 domain_idd1ny6a_
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family familyc.37.1.20 — Extended AAA-ATPase domain
结构域编号 domain_idd1ny6b_
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family familyc.37.1.20 — Extended AAA-ATPase domain
结构域编号 domain_idd1ny6c_
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family familyc.37.1.20 — Extended AAA-ATPase domain
结构域编号 domain_idd1ny6d_
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family familyc.37.1.20 — Extended AAA-ATPase domain
结构域编号 domain_idd1ny6e_
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family familyc.37.1.20 — Extended AAA-ATPase domain
结构域编号 domain_idd1ny6f_
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family familyc.37.1.20 — Extended AAA-ATPase domain
结构域编号 domain_idd1ny6g_
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family familyc.37.1.20 — Extended AAA-ATPase domain
结构域编号 domain_idd1ny6h_
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family familyc.37.1.20 — Extended AAA-ATPase domain
结构域编号 domain_idd1ny6i_
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family familyc.37.1.20 — Extended AAA-ATPase domain
结构域编号 domain_idd1ny6j_
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family familyc.37.1.20 — Extended AAA-ATPase domain
结构域编号 domain_idd1ny6k_
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family familyc.37.1.20 — Extended AAA-ATPase domain
结构域编号 domain_idd1ny6l_
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family familyc.37.1.20 — Extended AAA-ATPase domain
结构域编号 domain_idd1ny6m_
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family familyc.37.1.20 — Extended AAA-ATPase domain
结构域编号 domain_idd1ny6n_
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family familyc.37.1.20 — Extended AAA-ATPase domain

CATH v4.4 (28 domains)

结构域编号 domain_id1ny6A01
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
结构域编号 domain_id1ny6A02
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology8 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily60
结构域编号 domain_id1ny6B01
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
结构域编号 domain_id1ny6B02
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology8 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily60
结构域编号 domain_id1ny6C01
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
结构域编号 domain_id1ny6C02
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology8 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily60
结构域编号 domain_id1ny6D01
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
结构域编号 domain_id1ny6D02
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology8 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily60
结构域编号 domain_id1ny6E01
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
结构域编号 domain_id1ny6E02
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology8 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily60
结构域编号 domain_id1ny6F01
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
结构域编号 domain_id1ny6F02
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology8 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily60
结构域编号 domain_id1ny6G01
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
结构域编号 domain_id1ny6G02
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology8 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily60
结构域编号 domain_id1ny6H01
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
结构域编号 domain_id1ny6H02
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology8 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily60
结构域编号 domain_id1ny6I01
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
结构域编号 domain_id1ny6I02
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology8 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily60
结构域编号 domain_id1ny6J01
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
结构域编号 domain_id1ny6J02
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology8 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily60
结构域编号 domain_id1ny6K01
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
结构域编号 domain_id1ny6K02
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology8 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily60
结构域编号 domain_id1ny6L01
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
结构域编号 domain_id1ny6L02
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology8 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily60
结构域编号 domain_id1ny6M01
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
结构域编号 domain_id1ny6M02
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology8 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily60
结构域编号 domain_id1ny6N01
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
结构域编号 domain_id1ny6N02
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology8 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily60

8. 引用文献 (1)

9. 文件与曲线 (10)