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- PDB-1hi1: RNA dependent RNA polymerase from dsRNA bacteriophage phi6 plus b... -

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Basic information

Entry
Database: PDB / ID: 1hi1
TitleRNA dependent RNA polymerase from dsRNA bacteriophage phi6 plus bound NTP
ComponentsP2 PROTEIN
KeywordsRNA POLYMERASE / VIRAL POLYMERASE
Function / homology
Function and homology information


RNA uridylyltransferase activity / virion component / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / nucleotide binding / DNA-templated transcription / RNA binding / metal ion binding
Similarity search - Function
Phage p2 RNA dependent RNA polymerase domain / Alpha-Beta Plaits - #1600 / Dihydrolipoamide Transferase / Dihydrolipoamide Transferase - #10 / Cystovirus, RNA-directed RNA polymerase, N-terminal / Cystovirus, RNA-directed RNA polymerase / RNA-directed RNA polymerase, bacteriophage, catalytic domain / RdRp of RNA-containing bacteriophages catalytic domain profile. / Other non-globular / Globin-like ...Phage p2 RNA dependent RNA polymerase domain / Alpha-Beta Plaits - #1600 / Dihydrolipoamide Transferase / Dihydrolipoamide Transferase - #10 / Cystovirus, RNA-directed RNA polymerase, N-terminal / Cystovirus, RNA-directed RNA polymerase / RNA-directed RNA polymerase, bacteriophage, catalytic domain / RdRp of RNA-containing bacteriophages catalytic domain profile. / Other non-globular / Globin-like / Special / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Alpha-Beta Plaits / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / RNA-directed RNA polymerase
Similarity search - Component
Biological speciesBACTERIOPHAGE PHI-6 (bacteriophage)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsGrimes, J.M. / Butcher, S.J. / Makeyev, E.V. / Bamford, D.H. / Stuart, D.I.
Citation
Journal: Nature / Year: 2001
Title: A Mechanism for Initiating RNA-Dependent RNA Polymerization
Authors: Butcher, S.J. / Grimes, J.M. / Makeyev, E.V. / Bamford, D.H. / Stuart, D.I.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Crystallization and Preliminary X-Ray Crystallographic Studies on the Bacteriophage Phi6 RNA-Dependent RNA Polymerase
Authors: Butcher, S.J. / Makeyev, E.V. / Grimes, J.M. / Stuart, D.I. / Bamford, D.H.
History
DepositionJan 1, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 11, 2020Group: Advisory / Derived calculations / Category: pdbx_validate_close_contact / struct_conn
Revision 1.4May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: P2 PROTEIN
B: P2 PROTEIN
C: P2 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,2316
Polymers224,7103
Non-polymers1,5223
Water00
1
A: P2 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,4102
Polymers74,9031
Non-polymers5071
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: P2 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,4102
Polymers74,9031
Non-polymers5071
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: P2 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,4102
Polymers74,9031
Non-polymers5071
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)105.650, 92.700, 140.790
Angle α, β, γ (deg.)90.00, 101.09, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.13126, -0.71897, -0.68254), (-0.78577, -0.49523, 0.37056), (-0.60443, 0.48768, -0.62994)76.8858, 17.2982, 79.5172
2given(-0.16238, -0.7568, 0.63316), (0.77565, -0.49453, -0.39217), (0.60991, 0.42743, 0.66731)-59.1917, 6.5458, -28.1681

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Components

#1: Protein P2 PROTEIN / RNA-DIRECTED RNA POLYMERASE


Mass: 74903.203 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACTERIOPHAGE PHI-6 (bacteriophage) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P11124
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
Compound detailsP2 IS ONE OF THE 4 STRUCTURAL PROTEINS OF THE POLYHEDRAL PROCAPSID. IT IS RESPONSIBLE FOR GENOMIC ...P2 IS ONE OF THE 4 STRUCTURAL PROTEINS OF THE POLYHEDRAL PROCAPSID. IT IS RESPONSIBLE FOR GENOMIC REPLICATION AND TRANSCRIPTION.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

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Sample preparation

CrystalDensity Matthews: 3.01 Å3/Da / Density % sol: 59 %
Crystal growpH: 6.7
Details: 1:1 PROTEIN(5MG/ML)+TEMPLATE WELL SOLUTION: 10% PEG 8000, 0.1M MES, 2 MM MNCL2, pH 6.70
Crystal grow
*PLUS
Temperature: 293 K / Method: vapor diffusion, sitting drop
Details: Butcher, S.J., (2000) Acta Crystallogr.,Sect.D, 56, 1473.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
210 %PEG80001reservoir
30.1 MMEs1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9793
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 52305 / % possible obs: 97.7 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 9

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY TBA

Highest resolution: 3 Å
Details: ELECTRON DENSITY MAPS FOR 3 DATA SETS WERE FIRST INTERNALLY 3-FOLD AVERAGED AND THEN 3-FOLD CROSS-CRYSTAL AVERAGING CARRIED OUT BETWEEN THEM. THE MODEL WAS THEN BUILT INTO THIS FINAL 9-FOLD ...Details: ELECTRON DENSITY MAPS FOR 3 DATA SETS WERE FIRST INTERNALLY 3-FOLD AVERAGED AND THEN 3-FOLD CROSS-CRYSTAL AVERAGING CARRIED OUT BETWEEN THEM. THE MODEL WAS THEN BUILT INTO THIS FINAL 9-FOLD AVERAGED MAP. ONLY THE TRI-PHOSPHATE IS ORDERED IN THE NTP. THE PROTEIN MODEL WAS RIGID BODY REFINED AGAINST THE DATA SETS AND INITIAL PHASES CALCULATED FROM THIS PROTEIN MODEL THS COMPLEX IS OF THE RNA DEPENDENT RNA POLYMERASE WITH BOUND NTP. THREE DATA SETS WERE COLLECTED FROM THREE DIFFERENT NTP SOAKED CRYSTALS, AND PHASES CALCULATED FROM THE RIGID BODY REFINED MODEL OF THE 3 NON- CRYSTALLOGRAPHICALLY RELATED PROTEIN MOLECULES IN THE ASYMMETRIC UNIT. MAPS CALCULATED USING THESE PHASES WERE THEN INTERNALLY 3-FOLD AVERAGED. THE 3 MAPS WERE THEMSELVES AVERAGED TOGETHER TO PRODUCE A MAP IN WHICH CLEAR DENSITY FOR THE ORDERED TRI-PHOSPHATE WAS OBSERVED. THE MODEL FOR ATP WAS BUILT INTO THIS MAP, ALTHOUGH ONLY THE TRI-PHOSPHATE POSTION IS UNAMBIGUOUS. TO REFLECT THIS THE BFACTORS FOR THE TRI- PHOSPHATES ARE SET TO 20 AND THE REST OF THE ATOMS OF THE ATP MOLECULE SET TO 999
Refinement stepCycle: LAST / Highest resolution: 3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15795 0 93 0 15888
Refinement
*PLUS
Num. reflection obs: 50000 / Num. reflection Rfree: 3000 / Rfactor Rwork: 0.26
Solvent computation
*PLUS
Displacement parameters
*PLUS

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