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- PDB-1i9s: CRYSTAL STRUCTURE OF THE RNA TRIPHOSPHATASE DOMAIN OF MOUSE MRNA ... -

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Basic information

Entry
Database: PDB / ID: 1i9s
TitleCRYSTAL STRUCTURE OF THE RNA TRIPHOSPHATASE DOMAIN OF MOUSE MRNA CAPPING ENZYME
ComponentsMRNA CAPPING ENZYMEMRNA guanylyltransferase
KeywordsHYDROLASE / RNA triphosphatase domain / mRNA capping enzyme
Function / homology
Function and homology information


RNA Pol II CTD phosphorylation and interaction with CE / mRNA Capping / RNA guanylyltransferase activity / inorganic triphosphate phosphatase activity / mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / polynucleotide 5'-phosphatase activity / protein tyrosine/serine/threonine phosphatase activity / 7-methylguanosine mRNA capping / RNA processing ...RNA Pol II CTD phosphorylation and interaction with CE / mRNA Capping / RNA guanylyltransferase activity / inorganic triphosphate phosphatase activity / mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / polynucleotide 5'-phosphatase activity / protein tyrosine/serine/threonine phosphatase activity / 7-methylguanosine mRNA capping / RNA processing / dephosphorylation / mRNA guanylyltransferase activity / mRNA guanylyltransferase / GTP binding / ATP binding / nucleus
Similarity search - Function
mRNA capping enzyme, bifunctional / mRNA capping enzyme, adenylation domain / mRNA capping enzyme, C-terminal / mRNA capping enzyme, catalytic domain / mRNA capping enzyme, C-terminal domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain / Dual specificity protein phosphatase domain profile. / Protein tyrosine phosphatase superfamily ...mRNA capping enzyme, bifunctional / mRNA capping enzyme, adenylation domain / mRNA capping enzyme, C-terminal / mRNA capping enzyme, catalytic domain / mRNA capping enzyme, C-terminal domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain / Dual specificity protein phosphatase domain profile. / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / Nucleic acid-binding, OB-fold / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
CACODYLATE ION / ISOPROPYL ALCOHOL / mRNA-capping enzyme
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.65 Å
AuthorsChangela, A. / Ho, C.K. / Martins, A. / Shuman, S. / Mondragon, A.
CitationJournal: EMBO J. / Year: 2001
Title: Structure and mechanism of the RNA triphosphatase component of mammalian mRNA capping enzyme.
Authors: Changela, A. / Ho, C.K. / Martins, A. / Shuman, S. / Mondragon, A.
History
DepositionMar 20, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MRNA CAPPING ENZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6976
Polymers24,3201
Non-polymers3785
Water3,891216
1


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

A: MRNA CAPPING ENZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,39412
Polymers48,6392
Non-polymers75510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area2340 Å2
ΔGint-48 kcal/mol
Surface area18730 Å2
MethodPISA
3
A: MRNA CAPPING ENZYME
hetero molecules

A: MRNA CAPPING ENZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,39412
Polymers48,6392
Non-polymers75510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
MethodPQS
Unit cell
Length a, b, c (Å)62.228, 98.856, 71.818
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein MRNA CAPPING ENZYME / MRNA guanylyltransferase / MCE1


Mass: 24319.631 Da / Num. of mol.: 1 / Fragment: TPASE DOMAIN (RESIDUES 1-210)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PET16B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O55236, polynucleotide 5'-phosphatase

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Non-polymers , 5 types, 221 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate / Cacodylic acid


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H2O

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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: 2.27 Å3/Da / Density % sol: 45.8 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 15% isopropanol, 50mM sodium cacodylate (pH 6.5), 25mM magnesium chloride, 25mM ammonium sulfate , VAPOR DIFFUSION, HANGING DROP, temperature 283K
Crystal grow
*PLUS
Temperature: 10 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein1drop
215 %isopropanol1reservoir
350 mMsodium cacodylate1reservoir
425 mM1reservoirMgCl2
525 mMammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 15, 2000
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.65→27 Å / Num. all: 143292 / Num. obs: 26506 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 16.2 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 8.4 / Net I/σ(I): 5.2
Reflection shellResolution: 1.65→1.69 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.282 / Mean I/σ(I) obs: 2.9 / Num. unique all: 1916 / Rsym value: 25.1 / % possible all: 98.6
Reflection
*PLUS
Num. measured all: 143292
Reflection shell
*PLUS
% possible obs: 98.6 %

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Processing

Software
NameVersionClassification
MLPHAREphasing
REFMACrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.65→27 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.225 1334 random
Rwork0.194 --
all0.196 26497 -
obs0.196 26497 -
Refinement stepCycle: LAST / Resolution: 1.65→27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1536 0 17 216 1769
LS refinement shellResolution: 1.65→1.74 Å
RfactorNum. reflection
Rfree0.235 172
Rwork0.193 -
obs-3247
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.01
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.6
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_improper_angle_d
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scangle_it

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