1tug

Aspartate Transcarbamoylase Catalytic Chain Mutant E50A Complex with Phosphonoacetamide, Malonate, and Cytidine-5-Prime-Triphosphate (CTP)

Method: X-RAY DIFFRACTION Dmax: 104.0 Å Quality: GOOD

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

Aspartate carbamoyltransferase catalytic chain

Escherichia coli

UniProt P0A786

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 蛋白异源复合物 异源复合物 蛋白 × 12 PDB 声明:dodecameric(12) 与蛋白拷贝数一致 链 A; UniProt 1–310 链 C; UniProt 1–310 突变:E50A Aspartate carbamoyltransferase regulatory chain × 6 (P0A7F3) MLI MALONATE ION × 6 PCT PHOSPHONOACETAMIDE × 6 ZN ZINC ION × 6 CTP CYTIDINE-5'-TRIPHOSPHATE × 6 X-RAY DIFFRACTION X-ray结晶条件:pH 6;295 K;100 mM sodium citrate, 1 mM 2-mercaptoethanol, 0.2 mM EDTA and 1.0 mM CTP pH 6.0 then soaked for 24 hours in 100 mM malonate, 2 mM CTP, 3 mM sodium azide, 2 mM 2-mercaptoethanol, and 15% PEG 8000 pH 7.0. Before mounting, 50 mM PAM was added and the crystal allowed to soak until data collected., MICRODIALYSIS, temperature 295K, pH 6.00 分辨率 2.10 Å R-free 0.272

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 59 个其他 PDB 条目、61 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 PYRB_ECOLI
Isoform
PDB实体 1
链与序列区间 作者链 A; PDB构建体 1–310; UniProt 1–310 作者链 C; PDB构建体 1–310; UniProt 1–310

Aspartate carbamoyltransferase regulatory chain

Escherichia coli

UniProt P0A7F3

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 蛋白异源复合物 异源复合物 蛋白 × 12 PDB 声明:dodecameric(12) 与蛋白拷贝数一致 链 B; UniProt 1–152 链 D; UniProt 1–152 未记录 Aspartate carbamoyltransferase catalytic chain × 6 (P0A786) MLI MALONATE ION × 6 PCT PHOSPHONOACETAMIDE × 6 ZN ZINC ION × 6 CTP CYTIDINE-5'-TRIPHOSPHATE × 6 X-RAY DIFFRACTION X-ray结晶条件:pH 6;295 K;100 mM sodium citrate, 1 mM 2-mercaptoethanol, 0.2 mM EDTA and 1.0 mM CTP pH 6.0 then soaked for 24 hours in 100 mM malonate, 2 mM CTP, 3 mM sodium azide, 2 mM 2-mercaptoethanol, and 15% PEG 8000 pH 7.0. Before mounting, 50 mM PAM was added and the crystal allowed to soak until data collected., MICRODIALYSIS, temperature 295K, pH 6.00 分辨率 2.10 Å R-free 0.272

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 54 个其他 PDB 条目、55 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 PYRI_ECOLI
Isoform
PDB实体 2
链与序列区间 作者链 B; PDB构建体 2–153; UniProt 1–152 作者链 D; PDB构建体 2–153; UniProt 1–152

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 1tug

P(r) 距离分布 P(r) Distribution

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

条目编号 entry_id1tug
沉积日期 deposition_date2004-06-24
结构标题 titleAspartate Transcarbamoylase Catalytic Chain Mutant E50A Complex with Phosphonoacetamide, Malonate, and Cytidine-5-Prime-Triphosphate (CTP)
关键词 keywordsprotein structure-function, site specific mutagenesis, domain closure, allosteric transition, HYDROLASE-HYDROLASE REGULATOR COMPLEX; HYDROLASE/HYDROLASE REGULATOR
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_guinier37.69
回转半径 Rg (电子) rg_electron37.11
零角强度 I(0) i0171475000.00
分子量 molecular_weight104290.0 kDa
排除体积 excluded_volume130010 ų
包络体积 envelope_volume174780 ų
水化壳体积 shell_volume39768 ų
包络直径 envelope_diameter109.1
壳层 Rg shell_rg43.02
包络 Rg envelope_rg35.86
形状 Rg shape_rg37.12
总 Rg total_rg37.45
总原子数 total_atoms7314
残基数 n_residues926
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 dmax104.0
Rg (实空间) rg_real37.56
Rg 误差 (实空间) rg_real_error0.65
I(0) (实空间) i0_real1.7150e+08
I(0) 误差 (实空间) i0_real_error2.9180e+06
Rg (倒空间) rg_reciprocal37.65
I(0) (倒空间) i0_reciprocal171500000.0000
解质量估计 total_estimate0.8381
解质量评级 solution_quality GOOD a GOOD solution
P(r) 峰数 n_peaks2
主峰位置 r_peak_primary61.9
偏度 Skewness skewness0.024
峰度 Kurtosis kurtosis-0.907
角度范围 angular_range— – 0.2100 −1
当前正则化参数 α current_alpha0.0000
最高正则化参数 α highest_alpha19350000.0000
实空间数据点数 n_real_points43
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.000; Oscil: 0.990; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.920; Smooth: 0.001

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

6. 实体与聚合物信息 Entities & Polymers (7)

7. 折叠分类 (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

结构域编号 domain_idd1tuga1
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.78 — ATC-like
超家族 Superfamily superfamilyc.78.1 — Aspartate/ornithine carbamoyltransferase
家族 Family familyc.78.1.1 — Aspartate/ornithine carbamoyltransferase
结构域编号 domain_idd1tugb1
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.58 — Ferredoxin-like
超家族 Superfamily superfamilyd.58.2 — Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain
家族 Family familyd.58.2.1 — Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain
结构域编号 domain_idd1tugb2
类 Class classg — Small proteins
折叠类型 Fold foldg.41 — Rubredoxin-like
超家族 Superfamily superfamilyg.41.7 — Aspartate carbamoyltransferase, Regulatory-chain, C-terminal domain
家族 Family familyg.41.7.1 — Aspartate carbamoyltransferase, Regulatory-chain, C-terminal domain
结构域编号 domain_idd1tugc1
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.78 — ATC-like
超家族 Superfamily superfamilyc.78.1 — Aspartate/ornithine carbamoyltransferase
家族 Family familyc.78.1.1 — Aspartate/ornithine carbamoyltransferase
结构域编号 domain_idd1tugd1
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.58 — Ferredoxin-like
超家族 Superfamily superfamilyd.58.2 — Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain
家族 Family familyd.58.2.1 — Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain
结构域编号 domain_idd1tugd2
类 Class classg — Small proteins
折叠类型 Fold foldg.41 — Rubredoxin-like
超家族 Superfamily superfamilyg.41.7 — Aspartate carbamoyltransferase, Regulatory-chain, C-terminal domain
家族 Family familyg.41.7.1 — Aspartate carbamoyltransferase, Regulatory-chain, C-terminal domain

CATH v4.4 (8 domains)

结构域编号 domain_id1tugA01
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 superfamily1370 — Aspartate/ornithine carbamoyltransferase
结构域编号 domain_id1tugA02
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 superfamily1370 — Aspartate/ornithine carbamoyltransferase
结构域编号 domain_id1tugB01
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily140 — Aspartate carbamoyltransferase regulatory subunit, N-terminal domain
结构域编号 domain_id1tugB02
类 Class class2 — Mainly Beta
架构 Architecture architecture30 — Roll
拓扑 Topology topology30 — SH3 type barrels.
同源超家族 H-superfamily homologous superfamily20 — Aspartate carbamoyltransferase regulatory subunit, C-terminal domain
结构域编号 domain_id1tugC01
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 superfamily1370 — Aspartate/ornithine carbamoyltransferase
结构域编号 domain_id1tugC02
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 superfamily1370 — Aspartate/ornithine carbamoyltransferase
结构域编号 domain_id1tugD01
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily140 — Aspartate carbamoyltransferase regulatory subunit, N-terminal domain
结构域编号 domain_id1tugD02
类 Class class2 — Mainly Beta
架构 Architecture architecture30 — Roll
拓扑 Topology topology30 — SH3 type barrels.
同源超家族 H-superfamily homologous superfamily20 — Aspartate carbamoyltransferase regulatory subunit, C-terminal domain

8. 引用文献 (1)

9. 文件与曲线 (10)