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- PDB-2jl9: Structural explanation for the role of Mn in the activity of phi6... -

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Basic information

Entry
Database: PDB / ID: 2jl9
TitleStructural explanation for the role of Mn in the activity of phi6 RNA- dependent RNA polymerase
ComponentsRNA-DIRECTED RNA POLYMERASE
KeywordsTRANSFERASE / NUCLEOTIDE-BINDING / NUCLEOTIDYLTRANSFERASE / RNA-DEPENDENT RNA POLYMERASE / METAL-BINDING / OLIGONUCLEOTIDE / RNA-DIRECTED RNA POLYMERASE / RNA REPLICATION / POLYMERASE-COMPLEX / VIRION / MANGANESE / MAGNESIUM / POLYMERASE
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
RNA-directed RNA polymerase
Similarity search - Component
Biological speciesPSEUDOMONAS PHAGE PHI6 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 3.2 Å
AuthorsPoranen, M.M. / Salgado, P.S. / Koivunen, M.R.L. / Wright, S. / Bamford, D.H. / Stuart, D.I. / Grimes, J.M.
CitationJournal: Nucleic Acids Res. / Year: 2008
Title: Structural Explanation for the Role of Mn2+ in the Activity of {Phi}6 RNA-Dependent RNA Polymerase.
Authors: Poranen, M.M. / Salgado, P.S. / Koivunen, M.R.L. / Wright, S. / Bamford, D.H. / Stuart, D.I. / Grimes, J.M.
History
DepositionSep 5, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA-DIRECTED RNA POLYMERASE
B: RNA-DIRECTED RNA POLYMERASE
C: RNA-DIRECTED RNA POLYMERASE


Theoretical massNumber of molelcules
Total (without water)225,1003
Polymers225,1003
Non-polymers00
Water00
1
A: RNA-DIRECTED RNA POLYMERASE


Theoretical massNumber of molelcules
Total (without water)75,0331
Polymers75,0331
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: RNA-DIRECTED RNA POLYMERASE


Theoretical massNumber of molelcules
Total (without water)75,0331
Polymers75,0331
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: RNA-DIRECTED RNA POLYMERASE


Theoretical massNumber of molelcules
Total (without water)75,0331
Polymers75,0331
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)106.519, 91.599, 142.705
Angle α, β, γ (deg.)90.00, 101.64, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
12
22
32
13
23
33
14
24
34

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 3:30 OR RESSEQ 104:276 OR RESSEQ 333:397 )
211CHAIN B AND (RESSEQ 3:30 OR RESSEQ 104:276 OR RESSEQ 333:397 )
311CHAIN C AND (RESSEQ 3:30 OR RESSEQ 104:276 OR RESSEQ 333:397 )
112CHAIN A AND (RESSEQ 277:332 OR RESSEQ 398:517 )
212CHAIN B AND (RESSEQ 277:332 OR RESSEQ 398:517 )
312CHAIN C AND (RESSEQ 277:332 OR RESSEQ 398:517 )
113CHAIN A AND (RESSEQ 37:91 OR RESSEQ 518:600 )
213CHAIN B AND (RESSEQ 37:91 OR RESSEQ 518:600 )
313CHAIN C AND (RESSEQ 37:91 OR RESSEQ 518:600 )
114CHAIN A AND (RESSEQ 601:663 )
214CHAIN B AND (RESSEQ 601:663 )
314CHAIN C AND (RESSEQ 601:663 )

NCS ensembles :
ID
1
2
3
4

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Components

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


Mass: 75033.414 Da / Num. of mol.: 3 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS PHAGE PHI6 (virus) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P11124, RNA-directed RNA polymerase
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLU 492 TO GLN ENGINEERED RESIDUE IN CHAIN B, GLU 492 TO GLN ...ENGINEERED RESIDUE IN CHAIN A, GLU 492 TO GLN ENGINEERED RESIDUE IN CHAIN B, GLU 492 TO GLN ENGINEERED RESIDUE IN CHAIN C, GLU 492 TO GLN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.12 Å3/Da / Density % sol: 60.22 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.89
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.89 Å / Relative weight: 1
ReflectionResolution: 3.2→20 Å / Num. obs: 40323 / % possible obs: 91 % / Observed criterion σ(I): 0 / Redundancy: 11 % / Biso Wilson estimate: 52.39 Å2 / Rmerge(I) obs: 0.18 / Net I/σ(I): 7
Reflection shellResolution: 3.2→3.3 Å / % possible all: 81

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 3.2→19.915 Å / SU ML: 0.53 / σ(F): 1.35 / Phase error: 27.81 / Stereochemistry target values: ML / Details: SOME DISORDERED REGIONS WERE NOT BUILT
RfactorNum. reflection% reflection
Rfree0.272 2036 5.1 %
Rwork0.2148 --
obs0.2177 40090 90.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 9.13 Å2 / ksol: 0.3 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.279 Å20 Å22.0044 Å2
2---3.9924 Å20 Å2
3---2.7134 Å2
Refinement stepCycle: LAST / Resolution: 3.2→19.915 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15629 0 0 0 15629
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116017
X-RAY DIFFRACTIONf_angle_d1.2821667
X-RAY DIFFRACTIONf_dihedral_angle_d18.685873
X-RAY DIFFRACTIONf_chiral_restr0.082282
X-RAY DIFFRACTIONf_plane_restr02824
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2053X-RAY DIFFRACTIONPOSITIONAL
12B2053X-RAY DIFFRACTIONPOSITIONAL0.071
13C2053X-RAY DIFFRACTIONPOSITIONAL0.061
21A1412X-RAY DIFFRACTIONPOSITIONAL
22B1412X-RAY DIFFRACTIONPOSITIONAL0.056
23C1412X-RAY DIFFRACTIONPOSITIONAL0.057
31A1140X-RAY DIFFRACTIONPOSITIONAL
32B1140X-RAY DIFFRACTIONPOSITIONAL0.056
33C1140X-RAY DIFFRACTIONPOSITIONAL0.058
41A461X-RAY DIFFRACTIONPOSITIONAL
42B461X-RAY DIFFRACTIONPOSITIONAL0.053
43C453X-RAY DIFFRACTIONPOSITIONAL0.054
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2001-3.27420.40571220.34372134X-RAY DIFFRACTION76
3.2742-3.35570.33741210.31822242X-RAY DIFFRACTION81
3.3557-3.4460.37921070.28872304X-RAY DIFFRACTION82
3.446-3.54680.34221210.28732348X-RAY DIFFRACTION83
3.5468-3.66060.30521230.27982371X-RAY DIFFRACTION84
3.6606-3.79060.34491490.24832326X-RAY DIFFRACTION84
3.7906-3.94130.33161210.2332423X-RAY DIFFRACTION86
3.9413-4.11910.28631310.21392523X-RAY DIFFRACTION90
4.1191-4.33420.23251310.18552642X-RAY DIFFRACTION94
4.3342-4.60260.23681280.16452734X-RAY DIFFRACTION96
4.6026-4.95290.21741540.15992749X-RAY DIFFRACTION98
4.9529-5.44210.24241620.16852787X-RAY DIFFRACTION99
5.4421-6.20860.23651540.17572836X-RAY DIFFRACTION100
6.2086-7.74490.2451510.17082853X-RAY DIFFRACTION100
7.7449-19.91490.17831610.15762782X-RAY DIFFRACTION96

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