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- PDB-1wac: Back-priming mode of Phi6 RNA-dependent RNA polymerase -

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Basic information

Entry
Database: PDB / ID: 1wac
TitleBack-priming mode of Phi6 RNA-dependent RNA polymerase
ComponentsP2 PROTEIN
KeywordsPOLYMERASE / PHI6 RNA-DEPENDENT RNA POLYMERASE / TRANSCRIPTION
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
RNA-directed RNA polymerase
Similarity search - Component
Biological speciesPSEUDOMONAS PHAGE PHI-6 (bacteriophage)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsLaurila, M.R.L. / Salgado, P.S. / Stuart, D.I. / Grimes, J.M. / Bamford, D.H.
CitationJournal: J.Gen.Virol. / Year: 2005
Title: Back-Priming Mode of Phi6 RNA-Dependent RNA Polymerase
Authors: Laurila, M.R.L. / Salgado, P.S. / Stuart, D.I. / Grimes, J.M. / Bamford, D.H.
History
DepositionOct 26, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 27, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
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: P2 PROTEIN
B: P2 PROTEIN
C: P2 PROTEIN


Theoretical massNumber of molelcules
Total (without water)223,3223
Polymers223,3223
Non-polymers00
Water0
1
A: P2 PROTEIN


Theoretical massNumber of molelcules
Total (without water)74,4411
Polymers74,4411
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: P2 PROTEIN


Theoretical massNumber of molelcules
Total (without water)74,4411
Polymers74,4411
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: P2 PROTEIN


Theoretical massNumber of molelcules
Total (without water)74,4411
Polymers74,4411
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)76.579, 105.851, 157.712
Angle α, β, γ (deg.)90.00, 98.86, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.4818, -0.85426, -0.19523), (0.85655, -0.50613, 0.10077), (-0.1849, -0.11867, 0.97557)49.30606, 3.10159, -46.54394
2given(-0.49614, 0.8249, -0.27091), (-0.8457, -0.52977, -0.06428), (-0.19654, 0.19722, 0.96046)44.67166, 34.2141, -100.89204

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Components

#1: Protein P2 PROTEIN / PHI6 RNA-DEPENDENT RNA POLYMERASE


Mass: 74440.648 Da / Num. of mol.: 3 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS PHAGE PHI-6 (bacteriophage)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P11124
Compound detailsENGINEERED RESIDUE MET 465 ILE, CHAINS A, B, C DELETION MUTATION- QYKW (629-632) TO SG IN CHAINS A, ...ENGINEERED RESIDUE MET 465 ILE, CHAINS A, B, C DELETION MUTATION- QYKW (629-632) TO SG IN CHAINS A, B AND C. THE TWO RESIDUES WHICH HAVE BEEN INSERTED IN PLACE OF QYKW ARE MAPPED TO THEMSELVES IN THE DBREF RECORDS BELOW. P2 IS ONE OF THE 4 STRUCTURAL PROTEINS OF THE POLYHEDRAL PROCAPSID, WHICH IS RESPONSIBLE FOR GENOMIC REPLICATION AND TRANSCRIPTION.
Sequence detailsDELETION MUTATION- QYKW (629-632) TO SG IN CHAINS A, B AND C. THE TWO RESIDUES WHICH HAVE BEEN ...DELETION MUTATION- QYKW (629-632) TO SG IN CHAINS A, B AND C. THE TWO RESIDUES WHICH HAVE BEEN INSERTED IN PLACE OF QYKW ARE MAPPED TO THEMSELVES IN THE DBREF RECORDS BELOW.

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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: 2.83 Å3/Da / Density % sol: 50 %
Crystal growpH: 8
Details: 0.1M SODIUM CITRATE PH 5.6, 19% ISOPROPANOL, 19% PEG 4K, 5% GLYCEROL

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9756
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9756 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 57385 / % possible obs: 99.2 % / Observed criterion σ(I): 1.9 / Redundancy: 10.8 % / Biso Wilson estimate: 23.9 Å2 / Rmerge(I) obs: 0.02 / Net I/σ(I): 7.4
Reflection shellResolution: 3→3.1 Å / Mean I/σ(I) obs: 1.9 / % possible all: 98.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HI8

1hi8


Resolution: 3→20 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1769196.42 / Isotropic thermal model: RESTRAINED / Cross valid method: A POSTERIORI / σ(F): 0
Details: RESIDUES 1-5, 603-615, 626-634 BELONG TO DISORDERED LOOPS
RfactorNum. reflection% reflectionSelection details
Rfree0.28 2760 5.1 %RANDOM
Rwork0.241 ---
obs0.241 54620 99.2 %-
Solvent computationSolvent model: CNS BULK SOLVENT MODEL USED / Bsol: 45.2045 Å2 / ksol: 0.371779 e/Å3
Displacement parametersBiso mean: 35.65 Å2
Baniso -1Baniso -2Baniso -3
1-12.23 Å20 Å23.06 Å2
2---0.69 Å20 Å2
3----11.53 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.39 Å
Luzzati d res low-20 Å
Luzzati sigma a0.58 Å0.53 Å
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15693 0 0 0 15693
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.13
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.693
X-RAY DIFFRACTIONc_mcangle_it4.264
X-RAY DIFFRACTIONc_scbond_it5.114
X-RAY DIFFRACTIONc_scangle_it7.415
Refine LS restraints NCSNCS model details: CONSTRAINTS
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.363 458 5.6 %
Rwork0.336 7719 -
obs--98.8 %

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