1ckn

STRUCTURE OF GUANYLYLATED MRNA CAPPING ENZYME COMPLEXED WITH GTP

Method: X-RAY DIFFRACTION Dmax: 86.3 Å Quality: EXCELLENT

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

MRNA CAPPING ENZYME

Paramecium bursaria Chlorella virus 1

UniProt Q84424

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 蛋白单体 单体 蛋白 × 1 PDB 声明:monomeric(1) 与蛋白拷贝数一致 链 A; UniProt 1–330 非标准单体:是(mmCIF未提供具体位点) GTP GUANOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;pH 7.5;HANGING DROP VAPOR DIFFUSION. 10-15 MG/ML PROTEIN IN 50 MM TRIS-HCL, 0.5 M NACL, 10 MM MGCL2, 5MM GTP, 2 MM EDTA, 4 MM DTT, PH 7.5 WERE MIXED WITH AN EQUAL VOLUME OF AND EQUILIBRATED AGAINST 100 MM TRIS- HCL, 200 MM NACL, 200 MM AMMONIUM SULFATE, 34% MEOPEG 5000, PH 7.5. THE CRYSTALS WERE SOAKED IN EQUILIBRATION SOLUTION WITH 100 MM MANGANESE(II)CHLORIDE AND 5 MM GTP FOR 4 HOURS PRIOR TO DATA COLLECTION., vapor diffusion - hanging drop 分辨率 2.50 Å R-free 0.299
2 蛋白单体 单体 蛋白 × 1 PDB 声明:monomeric(1) 与蛋白拷贝数一致 链 B; UniProt 1–330 非标准单体:是(mmCIF未提供具体位点) MN MANGANESE (II) ION × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;pH 7.5;HANGING DROP VAPOR DIFFUSION. 10-15 MG/ML PROTEIN IN 50 MM TRIS-HCL, 0.5 M NACL, 10 MM MGCL2, 5MM GTP, 2 MM EDTA, 4 MM DTT, PH 7.5 WERE MIXED WITH AN EQUAL VOLUME OF AND EQUILIBRATED AGAINST 100 MM TRIS- HCL, 200 MM NACL, 200 MM AMMONIUM SULFATE, 34% MEOPEG 5000, PH 7.5. THE CRYSTALS WERE SOAKED IN EQUILIBRATION SOLUTION WITH 100 MM MANGANESE(II)CHLORIDE AND 5 MM GTP FOR 4 HOURS PRIOR TO DATA COLLECTION., vapor diffusion - hanging drop 分辨率 2.50 Å R-free 0.299
3 蛋白同源多聚体 同源多聚体 蛋白 × 2 PDB 声明:dimeric(2) 与蛋白拷贝数一致 链 A; UniProt 1–330 链 B; UniProt 1–330 非标准单体:是(mmCIF未提供具体位点) GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MN MANGANESE (II) ION × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;pH 7.5;HANGING DROP VAPOR DIFFUSION. 10-15 MG/ML PROTEIN IN 50 MM TRIS-HCL, 0.5 M NACL, 10 MM MGCL2, 5MM GTP, 2 MM EDTA, 4 MM DTT, PH 7.5 WERE MIXED WITH AN EQUAL VOLUME OF AND EQUILIBRATED AGAINST 100 MM TRIS- HCL, 200 MM NACL, 200 MM AMMONIUM SULFATE, 34% MEOPEG 5000, PH 7.5. THE CRYSTALS WERE SOAKED IN EQUILIBRATION SOLUTION WITH 100 MM MANGANESE(II)CHLORIDE AND 5 MM GTP FOR 4 HOURS PRIOR TO DATA COLLECTION., vapor diffusion - hanging drop 分辨率 2.50 Å R-free 0.299
4 蛋白同源多聚体 同源多聚体 蛋白 × 2 PDB 声明:dimeric(2) 与蛋白拷贝数一致 链 A; UniProt 1–330 非标准单体:是(mmCIF未提供具体位点) GTP GUANOSINE-5'-TRIPHOSPHATE × 2 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;pH 7.5;HANGING DROP VAPOR DIFFUSION. 10-15 MG/ML PROTEIN IN 50 MM TRIS-HCL, 0.5 M NACL, 10 MM MGCL2, 5MM GTP, 2 MM EDTA, 4 MM DTT, PH 7.5 WERE MIXED WITH AN EQUAL VOLUME OF AND EQUILIBRATED AGAINST 100 MM TRIS- HCL, 200 MM NACL, 200 MM AMMONIUM SULFATE, 34% MEOPEG 5000, PH 7.5. THE CRYSTALS WERE SOAKED IN EQUILIBRATION SOLUTION WITH 100 MM MANGANESE(II)CHLORIDE AND 5 MM GTP FOR 4 HOURS PRIOR TO DATA COLLECTION., vapor diffusion - hanging drop 分辨率 2.50 Å R-free 0.299

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 2 个其他 PDB 条目、7 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 MCE_9PHYC
Isoform
PDB实体 1, 2
链与序列区间 作者链 A; PDB构建体 1–330; UniProt 1–330 作者链 B; PDB构建体 1–330; UniProt 1–330

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 1ckn

P(r) 距离分布 P(r) Distribution

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

条目编号 entry_id1ckn
沉积日期 deposition_date1997-04-20
结构标题 titleSTRUCTURE OF GUANYLYLATED MRNA CAPPING ENZYME COMPLEXED WITH GTP
关键词 keywordsMRNA, CAPPING ENZYME, NUCLEOTIDYLTRANSFERASE; CAPPING ENZYME
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_guinier27.41
回转半径 Rg (电子) rg_electron26.77
零角强度 I(0) i082583000.00
分子量 molecular_weight73686.0 kDa
排除体积 excluded_volume93294 ų
包络体积 envelope_volume112190 ų
水化壳体积 shell_volume34537 ų
包络直径 envelope_diameter87.1
壳层 Rg shell_rg34.71
包络 Rg envelope_rg26.59
形状 Rg shape_rg26.76
总 Rg total_rg27.61
总原子数 total_atoms5183
残基数 n_residues633
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 dmax86.3
Rg (实空间) rg_real27.35
Rg 误差 (实空间) rg_real_error0.62
I(0) (实空间) i0_real8.2580e+07
I(0) 误差 (实空间) i0_real_error1.2120e+06
Rg (倒空间) rg_reciprocal27.37
I(0) (倒空间) i0_reciprocal82580000.0000
解质量估计 total_estimate0.9028
解质量评级 solution_quality EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks1
主峰位置 r_peak_primary31.2
偏度 Skewness skewness0.286
峰度 Kurtosis kurtosis-0.451
角度范围 angular_range— – 0.2900 −1
当前正则化参数 α current_alpha0.0000
最高正则化参数 α highest_alpha26850000.0000
实空间数据点数 n_real_points59
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.000; Oscil: 0.926; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.955

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

6. 实体与聚合物信息 Entities & Polymers (6)

7. 折叠分类 (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

结构域编号 domain_idd1ckna1
类 Class classb — All beta proteins
折叠类型 Fold foldb.40 — OB-fold
超家族 Superfamily superfamilyb.40.4 — Nucleic acid-binding proteins
家族 Family familyb.40.4.6 — DNA ligase/mRNA capping enzyme postcatalytic domain
结构域编号 domain_idd1ckna2
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.142 — ATP-grasp
超家族 Superfamily superfamilyd.142.2 — DNA ligase/mRNA capping enzyme, catalytic domain
家族 Family familyd.142.2.3 — mRNA capping enzyme
结构域编号 domain_idd1cknb1
类 Class classb — All beta proteins
折叠类型 Fold foldb.40 — OB-fold
超家族 Superfamily superfamilyb.40.4 — Nucleic acid-binding proteins
家族 Family familyb.40.4.6 — DNA ligase/mRNA capping enzyme postcatalytic domain
结构域编号 domain_idd1cknb2
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.142 — ATP-grasp
超家族 Superfamily superfamilyd.142.2 — DNA ligase/mRNA capping enzyme, catalytic domain
家族 Family familyd.142.2.3 — mRNA capping enzyme

CATH v4.4 (6 domains)

结构域编号 domain_id1cknA01
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology470 — D-amino Acid Aminotransferase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily30 — DNA ligase/mRNA capping enzyme
结构域编号 domain_id1cknA02
类 Class class2 — Mainly Beta
架构 Architecture architecture40 — Beta Barrel
拓扑 Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
同源超家族 H-superfamily homologous superfamily140 — Nucleic acid-binding proteins
结构域编号 domain_id1cknA03
类 Class class4 — Few Secondary Structures
架构 Architecture architecture10 — Irregular
拓扑 Topology topology87 — mRNA Capping Enzyme; Chain
同源超家族 H-superfamily homologous superfamily10 — mRNA Capping Enzyme; domain 3
结构域编号 domain_id1cknB01
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology470 — D-amino Acid Aminotransferase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily30 — DNA ligase/mRNA capping enzyme
结构域编号 domain_id1cknB02
类 Class class2 — Mainly Beta
架构 Architecture architecture40 — Beta Barrel
拓扑 Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
同源超家族 H-superfamily homologous superfamily140 — Nucleic acid-binding proteins
结构域编号 domain_id1cknB03
类 Class class4 — Few Secondary Structures
架构 Architecture architecture10 — Irregular
拓扑 Topology topology87 — mRNA Capping Enzyme; Chain
同源超家族 H-superfamily homologous superfamily10 — mRNA Capping Enzyme; domain 3

8. 引用文献 (2)

9. 文件与曲线 (10)