+Open data
-Basic information
Entry | Database: PDB / ID: 1ckn | ||||||
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Title | STRUCTURE OF GUANYLYLATED MRNA CAPPING ENZYME COMPLEXED WITH GTP | ||||||
Components | (MRNA CAPPING ...) x 2 | ||||||
Keywords | CAPPING ENZYME / MRNA / NUCLEOTIDYLTRANSFERASE | ||||||
Function / homology | Function and homology information 7-methylguanosine mRNA capping / mRNA guanylyltransferase activity / mRNA guanylyltransferase / GTP binding / ATP binding Similarity search - Function | ||||||
Biological species | Paramecium bursaria Chlorella virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å | ||||||
Authors | Hakansson, K. / Doherty, A.J. / Wigley, D.B. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 1997 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: Journal: To be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ckn.cif.gz | 145.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ckn.ent.gz | 116.9 KB | Display | PDB format |
PDBx/mmJSON format | 1ckn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ckn_validation.pdf.gz | 783.5 KB | Display | wwPDB validaton report |
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Full document | 1ckn_full_validation.pdf.gz | 799.7 KB | Display | |
Data in XML | 1ckn_validation.xml.gz | 30.5 KB | Display | |
Data in CIF | 1ckn_validation.cif.gz | 42.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ck/1ckn ftp://data.pdbj.org/pub/pdb/validation_reports/ck/1ckn | HTTPS FTP |
-Related structure data
Related structure data | 1ckmSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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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.) Paramecium bursaria Chlorella virus 1 / Genus: Chlorovirus / Production host: Escherichia coli (E. coli) / References: UniProt: Q84424, mRNA guanylyltransferase |
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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.) Paramecium bursaria Chlorella virus 1 / Genus: Chlorovirus / Production host: Escherichia coli (E. coli) / References: UniProt: Q84424, mRNA guanylyltransferase |
-Non-polymers , 4 types, 345 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
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 |
-Processing
Software |
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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: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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