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- PDB-4a8f: Non-Catalytic Ions Direct the RNA-Dependent RNA Polymerase of Bac... -

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Basic information

Entry
Database: PDB / ID: 4a8f
TitleNon-Catalytic Ions Direct the RNA-Dependent RNA Polymerase of Bacterial dsRNA virus phi6 from De Novo Initiation to Elongation
Components
  • 5'-D(*DAP*GP*CP*GP)-3'
  • RNA-DIRECTED RNA POLYMERASE
KeywordsTRANSFERASE / TRANSLATION
Function / homology
Function and homology information


RNA uridylyltransferase activity / virion component / RNA-directed RNA polymerase / viral RNA genome replication / nucleotide binding / RNA-directed RNA polymerase activity / 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 / DNA / RNA-directed RNA polymerase
Similarity search - Component
Biological speciesPSEUDOMONAS PHAGE PHI6 (virus)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsWright, S. / Poranen, M.M. / Bamford, D.H. / Stuart, D.I. / Grimes, J.M.
CitationJournal: J.Virol. / Year: 2012
Title: Noncatalytic Ions Direct the RNA-Dependent RNA Polymerase of Bacterial Double-Stranded RNA Virus Phi6 from De Novo Initiation to Elongation.
Authors: Wright, S. / Poranen, M.M. / Bamford, D.H. / Stuart, D.I. / Grimes, J.M.
History
DepositionNov 21, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 4, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _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

Downloads & links

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Assembly

Deposited unit
A: RNA-DIRECTED RNA POLYMERASE
B: RNA-DIRECTED RNA POLYMERASE
C: RNA-DIRECTED RNA POLYMERASE
G: 5'-D(*DAP*GP*CP*GP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,43513
Polymers226,3194
Non-polymers3,1169
Water00
1
A: RNA-DIRECTED RNA POLYMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,0734
Polymers75,0341
Non-polymers1,0393
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RNA-DIRECTED RNA POLYMERASE
G: 5'-D(*DAP*GP*CP*GP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,2895
Polymers76,2502
Non-polymers1,0393
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: RNA-DIRECTED RNA POLYMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,0734
Polymers75,0341
Non-polymers1,0393
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)105.915, 91.766, 140.461
Angle α, β, γ (deg.)90.00, 101.25, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 75034.398 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS PHAGE PHI6 (virus) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P11124, RNA-directed RNA polymerase
#2: DNA chain 5'-D(*DAP*GP*CP*GP)-3'


Mass: 1215.843 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
Sequence detailsTHE MET 465 (ILE 457) CONFLICT IS OWING TO A SEQUENCE DIFFERENCE (CONFIRMED EXPERIMENTALLY) FROM ...THE MET 465 (ILE 457) CONFLICT IS OWING TO A SEQUENCE DIFFERENCE (CONFIRMED EXPERIMENTALLY) FROM THAT IN THE UNIPROT ENTRY.

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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: 2.96 Å3/Da / Density % sol: 58.43 % / Description: NONE
Crystal growDetails: 20% PEG 4000, 100 MM HEPES (PH 7.5), 8.5% ISOPROPANOL, 15% GLYCEROL, 2 MM MNCL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.978
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 39855 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 71.66 Å2 / Rmerge(I) obs: 0.27 / Net I/σ(I): 6.3
Reflection shellResolution: 3.3→3.4 Å / Mean I/σ(I) obs: 1.7 / % possible all: 100

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Processing

SoftwareName: BUSTER / Version: 2.9.2 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HHS

1hhs


Resolution: 3.3→46.01 Å / Cor.coef. Fo:Fc: 0.8593 / Cor.coef. Fo:Fc free: 0.8193 / Cross valid method: THROUGHOUT / σ(F): 0
Details: REFINEMENT NOTE 1: IDEAL-DIST CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=MG ATP. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=15876. NUMBER WITH APPROX DEFAULT CCP4 ATOM ...Details: REFINEMENT NOTE 1: IDEAL-DIST CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=MG ATP. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=15876. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=168. NUMBER TREATED BY BAD NON- BONDED CONTACTS=4. DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.2896 2000 5 %RANDOM
Rwork0.2427 ---
obs0.2451 39842 100 %-
Displacement parametersBiso mean: 75.22 Å2
Baniso -1Baniso -2Baniso -3
1-0.6526 Å20 Å218.5173 Å2
2---32.3556 Å20 Å2
3---31.703 Å2
Refinement stepCycle: LAST / Resolution: 3.3→46.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15795 81 171 0 16047
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.01516456HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.3622316HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5774SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes404HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2384HARMONIC5
X-RAY DIFFRACTIONt_it16456HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.41
X-RAY DIFFRACTIONt_other_torsion20.1
X-RAY DIFFRACTIONt_improper_torsion20HARMONIC0
X-RAY DIFFRACTIONt_chiral_improper_torsion2016SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact19263SEMIHARMONIC4
LS refinement shellResolution: 3.3→3.39 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.5839 137 5.02 %
Rwork0.5111 2590 -
all0.5148 2727 -
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.76350.2720.33880.1779-0.01740.7192-0.03330.18590.08240.0761-0.0133-0.011-0.0068-0.01320.0466-0.0903-0.0136-0.10090.01970.1009-0.09269.325-0.182128.3898
20.51720.14050.39680.62580.10540.4460.00540.0222-0.06280.06840.0201-0.0072-0.0290.026-0.0255-0.0085-0.0037-0.05580.0162-0.0592-0.170958.802920.652755.6208
30.4416-0.2845-0.16150.3760.32521.21140.01180.02550.0031-0.0079-0.05260.0555-0.0958-0.0340.0408-0.00330.0211-0.0371-0.1344-0.0358-0.0837-42.61752.7425-3.1842
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESIDUES 1-664)
2X-RAY DIFFRACTION2(CHAIN B AND RESIDUES 1-664)
3X-RAY DIFFRACTION3(CHAIN C AND RESIDUES 1-664)

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