4fyx

E. coli Aspartate Transcarbamoylase complexed with dCTP, UTP, and Mg2+

Method: X-RAY DIFFRACTION Dmax: 108.7 Å Quality: GOOD

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

Aspartate carbamoyltransferase catalytic chain

物种未注明

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 2–311 链 C; UniProt 2–311 未记录 Aspartate carbamoyltransferase regulatory chain × 6 (P0A7F3) ZN ZINC ION × 6 UTP URIDINE 5'-TRIPHOSPHATE × 6 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 6 MG MAGNESIUM ION × 6 X-RAY DIFFRACTION X-ray结晶条件:MICRODIALYSIS;pH 5.7;298 K;40 mM sodium citrate, 1 mM 2-mercaptoethanol, 0.2 mM EDTA, 1.0 mM dCTP, pH 5.7 (crystals soaked in 5 mM UTP and 5 mM Mg2+), MICRODIALYSIS, temperature 298K 分辨率 2.09 Å R-free 0.212

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 2–311 作者链 C; PDB构建体 1–310; UniProt 2–311

Aspartate carbamoyltransferase regulatory chain

物种未注明

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 1–153 链 D; UniProt 1–153 未记录 Aspartate carbamoyltransferase catalytic chain × 6 (P0A786) ZN ZINC ION × 6 UTP URIDINE 5'-TRIPHOSPHATE × 6 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 6 MG MAGNESIUM ION × 6 X-RAY DIFFRACTION X-ray结晶条件:MICRODIALYSIS;pH 5.7;298 K;40 mM sodium citrate, 1 mM 2-mercaptoethanol, 0.2 mM EDTA, 1.0 mM dCTP, pH 5.7 (crystals soaked in 5 mM UTP and 5 mM Mg2+), MICRODIALYSIS, temperature 298K 分辨率 2.09 Å R-free 0.212

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 1–153; UniProt 1–153 作者链 D; PDB构建体 1–153; UniProt 1–153

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 4fyx

P(r) 距离分布 P(r) Distribution

P(r) distribution for 4fyx
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2. 结构基本信息 2. Structure Basics

条目编号 entry_id4fyx
沉积日期 deposition_date2012-07-05
结构标题 titleE. coli Aspartate Transcarbamoylase complexed with dCTP, UTP, and Mg2+
关键词 keywordspyrimidine nucleotide biosynthesis, feedback inhibition, allostery, TRANSFERASE; TRANSFERASE
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_guinier37.51
回转半径 Rg (电子) rg_electron36.86
零角强度 I(0) i0170812000.00
分子量 molecular_weight103690.0 kDa
排除体积 excluded_volume129150 ų
包络体积 envelope_volume172100 ų
水化壳体积 shell_volume39463 ų
包络直径 envelope_diameter108.1
壳层 Rg shell_rg42.67
包络 Rg envelope_rg35.51
形状 Rg shape_rg36.86
总 Rg total_rg37.24
总原子数 total_atoms7267
残基数 n_residues916
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 dmax108.7
Rg (实空间) rg_real37.37
Rg 误差 (实空间) rg_real_error0.91
I(0) (实空间) i0_real1.7080e+08
I(0) 误差 (实空间) i0_real_error2.8790e+06
Rg (倒空间) rg_reciprocal37.46
I(0) (倒空间) i0_reciprocal170800000.0000
解质量估计 total_estimate0.8641
解质量评级 solution_quality GOOD a GOOD solution
P(r) 峰数 n_peaks2
主峰位置 r_peak_primary62.1
偏度 Skewness skewness0.021
峰度 Kurtosis kurtosis-0.901
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_alpha16630000.0000
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: 0.968; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.974; Smooth: 0.353

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) 16 domains

SCOP 2.08 (8 domains)

结构域编号 domain_idd4fyxa1
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_idd4fyxa2
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_idd4fyxb1
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_idd4fyxb2
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_idd4fyxc1
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_idd4fyxc2
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_idd4fyxd1
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_idd4fyxd2
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_id4fyxA01
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_id4fyxA02
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_id4fyxB01
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_id4fyxB02
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_id4fyxC01
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_id4fyxC02
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_id4fyxD01
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_id4fyxD02
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)