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- PDB-2jlg: STRUCTURAL EXPLANATION FOR THE ROLE OF MN IN THE ACTIVITY OF PHI6... -

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Basic information

Entry
Database: PDB / ID: 2jlg
TitleSTRUCTURAL EXPLANATION FOR THE ROLE OF MN IN THE ACTIVITY OF PHI6 RNA-DEPENDENT RNA POLYMERASE
Components
  • 5'-D(*DT DT DT DC DCP)-3'
  • RNA-DIRECTED RNA POLYMERASE
KeywordsTRANSFERASE / NUCLEOTIDYLTRANSFERASE / RNA-DIRECTED RNA POLYMERASE / METAL-BINDING / RNA POLYMERASE / RNA REPLICATION / VIRION / MANGANESE / MAGNESIUM / VIRAL POLYMERASE / NUCLEOTIDE-BINDING
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
GUANOSINE-5'-TRIPHOSPHATE / : / DNA / RNA-directed RNA polymerase
Similarity search - Component
Biological speciesPSEUDOMONAS PHAGE PHI6 (bacteriophage)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 9, 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 1.3Dec 13, 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_conn
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_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

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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
D: 5'-D(*DT DT DT DC DCP)-3'
E: 5'-D(*DT DT DT DC DCP)-3'
F: 5'-D(*DT DT DT DC DCP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,19211
Polymers229,0456
Non-polymers2,1485
Water00
1
A: RNA-DIRECTED RNA POLYMERASE
D: 5'-D(*DT DT DT DC DCP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,8713
Polymers76,3482
Non-polymers5231
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-2 kcal/mol
Surface area25960 Å2
MethodPISA
2
B: RNA-DIRECTED RNA POLYMERASE
E: 5'-D(*DT DT DT DC DCP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,8713
Polymers76,3482
Non-polymers5231
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2640 Å2
ΔGint-10 kcal/mol
Surface area25620 Å2
MethodPISA
3
C: RNA-DIRECTED RNA POLYMERASE
F: 5'-D(*DT DT DT DC DCP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,4505
Polymers76,3482
Non-polymers1,1013
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-14 kcal/mol
Surface area24800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.026, 109.026, 158.835
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 3:69 OR RESSEQ 73: 208 OR...
211CHAIN B AND (RESSEQ 3:69 OR RESSEQ 73: 208 OR...

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Components

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


Mass: 74902.219 Da / Num. of mol.: 3 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS PHAGE PHI6 (bacteriophage) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P11124, RNA-directed RNA polymerase
#2: DNA chain 5'-D(*DT DT DT DC DCP)-3'


Mass: 1445.985 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) PSEUDOMONAS PHAGE PHI6 (bacteriophage)
#3: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
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
Sequence detailsGLU 491 HAS BEEN MUTATED TO GLN

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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: 2.4 Å3/Da / Density % sol: 48.7 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 52552 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 34.05 Å2 / Rmerge(I) obs: 0.21 / Net I/σ(I): 5.9
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4.2 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 1.2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HHS

1hhs


Resolution: 2.8→19.944 Å / SU ML: 0.53 / σ(F): 1.96 / Phase error: 30.58 / Stereochemistry target values: ML
Details: SOME BADLY DISORDERED REGIONS IN MOLECULE C WERE NOT MODELLED.
RfactorNum. reflection% reflection
Rfree0.2947 2641 5.11 %
Rwork0.2156 --
obs0.2196 51726 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 13.021 Å2 / ksol: 0.326 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.3782 Å2-0 Å20 Å2
2---0.3782 Å20 Å2
3---0.7563 Å2
Refinement stepCycle: LAST / Resolution: 2.8→19.944 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15705 265 129 0 16099
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d016523
X-RAY DIFFRACTIONf_angle_d1.322429
X-RAY DIFFRACTIONf_dihedral_angle_d20.196105
X-RAY DIFFRACTIONf_chiral_restr0.092355
X-RAY DIFFRACTIONf_plane_restr02860
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A4949X-RAY DIFFRACTIONPOSITIONAL
12B4949X-RAY DIFFRACTIONPOSITIONAL0.077
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8001-2.85090.37011270.30272560X-RAY DIFFRACTION100
2.8509-2.90560.36751550.28062622X-RAY DIFFRACTION100
2.9056-2.96470.35821500.27652608X-RAY DIFFRACTION100
2.9647-3.0290.34461170.26192614X-RAY DIFFRACTION100
3.029-3.09920.31471310.2732554X-RAY DIFFRACTION100
3.0992-3.17640.33991470.26032556X-RAY DIFFRACTION100
3.1764-3.26190.38021510.26092609X-RAY DIFFRACTION100
3.2619-3.35740.32971330.25692588X-RAY DIFFRACTION100
3.3574-3.46530.32581510.2332579X-RAY DIFFRACTION100
3.4653-3.58840.3041460.22292573X-RAY DIFFRACTION100
3.5884-3.73120.26531250.20132585X-RAY DIFFRACTION100
3.7312-3.89980.29441330.19512621X-RAY DIFFRACTION100
3.8998-4.10380.29221430.1912582X-RAY DIFFRACTION100
4.1038-4.35840.26461470.17242587X-RAY DIFFRACTION100
4.3584-4.69080.21921520.15932543X-RAY DIFFRACTION100
4.6908-5.15550.24531370.15082602X-RAY DIFFRACTION100
5.1555-5.88470.23861230.15942595X-RAY DIFFRACTION99
5.8847-7.35180.22631400.15892545X-RAY DIFFRACTION99
7.3518-19.94420.21031330.14972562X-RAY DIFFRACTION99

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