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- PDB-1cko: STRUCTURE OF MRNA CAPPING ENZYME IN COMPLEX WITH THE CAP ANALOG GPPPG -

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Basic information

Entry
Database: PDB / ID: 1cko
TitleSTRUCTURE OF MRNA CAPPING ENZYME IN COMPLEX WITH THE CAP ANALOG GPPPG
ComponentsMRNA CAPPING ENZYME
KeywordsCAPPING 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
mRNA Capping Enzyme; Chain / mRNA Capping Enzyme; domain 3 / mRNA capping enzyme, adenylation domain / mRNA capping enzyme, C-terminal / mRNA capping enzyme, catalytic domain / mRNA capping enzyme, C-terminal domain / : / DNA ligase/mRNA capping enzyme / D-amino Acid Aminotransferase; Chain A, domain 1 / Nucleic acid-binding proteins ...mRNA Capping Enzyme; Chain / mRNA Capping Enzyme; domain 3 / mRNA capping enzyme, adenylation domain / mRNA capping enzyme, C-terminal / mRNA capping enzyme, catalytic domain / mRNA capping enzyme, C-terminal domain / : / DNA ligase/mRNA capping enzyme / D-amino Acid Aminotransferase; Chain A, domain 1 / Nucleic acid-binding proteins / Few Secondary Structures / Irregular / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
DIGUANOSINE-5'-TRIPHOSPHATE / mRNA-capping enzyme
Similarity search - Component
Biological speciesParamecium bursaria Chlorella virus 1
MethodX-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
AuthorsHakansson, 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
DepositionSep 6, 1997Processing site: BNL
Revision 1.0Jan 28, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MRNA CAPPING ENZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7393
Polymers37,8851
Non-polymers8542
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: MRNA CAPPING ENZYME
hetero molecules

A: MRNA CAPPING ENZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,4786
Polymers75,7702
Non-polymers1,7084
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area3040 Å2
ΔGint-63 kcal/mol
Surface area31970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.476, 164.013, 103.502
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein MRNA CAPPING ENZYME / RNA GUANYLYLTRANSFERASE


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
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GP3 / DIGUANOSINE-5'-TRIPHOSPHATE


Mass: 788.406 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H27N10O18P3

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.4 Å3/Da / Density % sol: 72 %
Crystal growMethod: 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
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlenzyme11
21.3 mMGpppG11
350 mMTris11
4400 mM11NaCl
52 mMEDTA11
64 mMDTT11
750 mMpotassium phosphate12
85-10 %PEG800012
92 mM12ZnCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.448
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 1, 1997
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.448 Å / Relative weight: 1
ReflectionResolution: 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

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Processing

Software
NameClassification
AMoREphasing
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod 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

1ckm


Resolution: 3.1→10 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.314 -8 %
Rwork0.233 --
obs0.233 11642 96.7 %
Displacement parametersBiso mean: 72 Å2
Refinement stepCycle: LAST / Resolution: 3.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2561 0 52 0 2613
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.169
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.98
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.575
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19.PROTOPH19.PEP
X-RAY DIFFRACTION2PARAM19.SOLUSER DEFINED
X-RAY DIFFRACTION3USER DEFINED
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.985
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.575

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