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Open data
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Basic information
Entry | Database: PDB / ID: 1ckn | ||||||
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Title | STRUCTURE OF GUANYLYLATED MRNA CAPPING ENZYME COMPLEXED WITH GTP | ||||||
![]() | (MRNA CAPPING ...) x 2 | ||||||
![]() | CAPPING ENZYME / MRNA / NUCLEOTIDYLTRANSFERASE | ||||||
Function / homology | ![]() 7-methylguanosine mRNA capping / mRNA guanylyltransferase activity / mRNA guanylyltransferase / GTP binding / ATP binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Hakansson, K. / Doherty, A.J. / Wigley, D.B. | ||||||
![]() | ![]() Title: X-ray crystallography reveals a large conformational change during guanyl transfer by mRNA capping enzymes. Authors: Hakansson, K. / Doherty, A.J. / Shuman, S. / Wigley, D.B. #1: ![]() Title: Crystallization of the RNA Guanylyltransferase of Chlorella Virus Pbcv-1 Change During Guanyl Transfer by Mrna Capping Enzymes Authors: Doherty, A.J. / Hakansson, K. / Ho, C.K. / Shuman, S. / Wigley, D.B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 145.4 KB | Display | ![]() |
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PDB format | ![]() | 116.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 783.5 KB | Display | ![]() |
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Full document | ![]() | 799.7 KB | Display | |
Data in XML | ![]() | 30.5 KB | Display | |
Data in CIF | ![]() | 42.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ckmSC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 |
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4 | ![]()
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Unit cell |
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Components
-MRNA CAPPING ... , 2 types, 2 molecules AB
#1: Protein | Mass: 37884.992 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 38229.184 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Non-polymers , 4 types, 345 molecules ![](data/chem/img/GTP.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-GTP / |
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#4: Chemical | ChemComp-MN / |
#5: Chemical | ChemComp-SO4 / |
#6: Water | ChemComp-HOH / |
-Details
Compound details | THE TWO MOLECULES IN THE ASYMMETRIC UNIT ARE IN DIFFERENT CONFORMATIONS. THE PROTEIN IS MONOMERIC ...THE TWO MOLECULES IN THE ASYMMETRIC |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.5 Å3/Da / Density % sol: 65 % Description: THE POLYPEPTIDE CHAIN OF 1CKM WAS USED AS INITIAL MODEL. THE SAME SELECTION OF DATA FOR MONITORING THE FREE R WAS USED. | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.5 Details: 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 ...Details: 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 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknown / Details: Doherty, A.J., (1996) Nucl. Acids Res., 24. 2281. | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 1997 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→15 Å / Num. obs: 36109 / % possible obs: 97.6 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 48.3 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 13.1 |
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Processing
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Refinement | Starting model: PDB ENTRY 1CKM Resolution: 2.5→10 Å / σ(F): 0
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Displacement parameters | Biso mean: 29 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→10 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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