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Yorodumi- PDB-1cko: STRUCTURE OF MRNA CAPPING ENZYME IN COMPLEX WITH THE CAP ANALOG GPPPG -
+Open data
-Basic information
Entry | Database: PDB / ID: 1cko | ||||||
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Title | STRUCTURE OF MRNA CAPPING ENZYME IN COMPLEX WITH THE CAP ANALOG GPPPG | ||||||
Components | MRNA CAPPING ENZYME | ||||||
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 / MOLECULAR REPLACEMENT. THE ROTATION FUNCTION WAS SOLVED FOR EACH OF THE TWO DOMAINS SEPARATELY. TRANSLATION WAS PERFORMED WITH THE TWO DOMAINS INDEPENDENTLY BUT SIMULTANEOUSLY. / Resolution: 3.1 Å | ||||||
Authors | Hakansson, K. / Wigley, D.B. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1998 Title: Structure of a complex between a cap analogue and mRNA guanylyl transferase demonstrates the structural chemistry of RNA capping. Authors: Hakansson, K. / Wigley, D.B. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1997 Title: Crystallization of the RNA Guanylyltransferase of Chlorella Virus Pbcv-1 Authors: Doherty, A.J. / Hakansson, K. / Ho, C.K. / Shuman, S. / Wigley, D.B. #2: 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1cko.cif.gz | 78.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cko.ent.gz | 59.5 KB | Display | PDB format |
PDBx/mmJSON format | 1cko.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1cko_validation.pdf.gz | 741.7 KB | Display | wwPDB validaton report |
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Full document | 1cko_full_validation.pdf.gz | 755.7 KB | Display | |
Data in XML | 1cko_validation.xml.gz | 15.5 KB | Display | |
Data in CIF | 1cko_validation.cif.gz | 20.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ck/1cko ftp://data.pdbj.org/pub/pdb/validation_reports/ck/1cko | HTTPS FTP |
-Related structure data
Related structure data | 1ckmS S: Starting model for refinement |
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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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Unit cell |
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-Components
#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: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-GP3 / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.4 Å3/Da / Density % sol: 72 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6.5 Details: HANGING DROP VAPOR DIFFUSION. 15 MG/ML PROTEIN IN 50 MM TRIS-HCL, 1.3 MM CAP ANALOG (GPPPG) 0.4 M NACL, 2 MM EDTA, 4 MM DTT, PH 7.5 WERE MIXED WITH AN EQUAL VOLUME OF AND EQUILIBRATED ...Details: HANGING DROP VAPOR DIFFUSION. 15 MG/ML PROTEIN IN 50 MM TRIS-HCL, 1.3 MM CAP ANALOG (GPPPG) 0.4 M NACL, 2 MM EDTA, 4 MM DTT, PH 7.5 WERE MIXED WITH AN EQUAL VOLUME OF AND EQUILIBRATED AGAINST 50 MM POTASSIUM PHOSPHATE, 5-10% PEG 8000, 2MM ZNCL2 PH 6.5., vapor diffusion - hanging drop PH range: 6.5-7.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: PX7.2 / Wavelength: 1.448 |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 1, 1997 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.448 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→20 Å / Num. obs: 12014 / % possible obs: 96.8 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 107 Å2 / Rmerge(I) obs: 0.035 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT. THE ROTATION FUNCTION WAS SOLVED FOR EACH OF THE TWO DOMAINS SEPARATELY. TRANSLATION WAS PERFORMED WITH THE TWO DOMAINS INDEPENDENTLY BUT SIMULTANEOUSLY. Starting model: OPEN FORM OF PDB ENTRY 1CKM Resolution: 3.1→10 Å / σ(F): 0
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Displacement parameters | Biso mean: 72 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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