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- PDB-1hht: RNA dependent RNA polymerase from dsRNA bacteriophage phi6 plus t... -

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Basic information

Entry
Database: PDB / ID: 1hht
TitleRNA dependent RNA polymerase from dsRNA bacteriophage phi6 plus template
Components
  • DNA (5'-(*TP*TP*TP*CP*C)-3')
  • P2 PROTEIN
KeywordsRNA POLYMERASE / VIRAL 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
: / DNA / RNA-directed RNA polymerase
Similarity search - Component
Biological speciesBACTERIOPHAGE PHI-6 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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
DepositionDec 28, 2000Deposition 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 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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 / _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
D: DNA (5'-(*TP*TP*TP*CP*C)-3')
E: DNA (5'-(*TP*TP*TP*CP*C)-3')
F: DNA (5'-(*TP*TP*TP*CP*C)-3')
P: P2 PROTEIN
Q: P2 PROTEIN
R: P2 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,2129
Polymers229,0486
Non-polymers1653
Water00
1
D: DNA (5'-(*TP*TP*TP*CP*C)-3')
P: P2 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,4043
Polymers76,3492
Non-polymers551
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
E: DNA (5'-(*TP*TP*TP*CP*C)-3')
Q: P2 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,4043
Polymers76,3492
Non-polymers551
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
F: DNA (5'-(*TP*TP*TP*CP*C)-3')
R: P2 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,4043
Polymers76,3492
Non-polymers551
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)105.089, 92.239, 140.640
Angle α, β, γ (deg.)90.00, 101.04, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.12942, -0.72181, -0.67988), (-0.79192, -0.48787, 0.36722), (-0.59676, 0.49089, -0.63475)76.84791, 17.24094, 79.68494
2given(-0.16472, -0.75473, 0.63502), (0.779, -0.49445, -0.38559), (0.605, 0.43117, 0.66938)-59.14212, 6.50602, -28.28033
DetailsTHE PROTEIN IS ACTIVE AS A MONOMER

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Components

#1: DNA chain DNA (5'-(*TP*TP*TP*CP*C)-3')


Mass: 1445.985 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: 5 NUCLEOTIDE DNA VERSION OF OPTIMUM RNA TEMPLATE
#2: 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 (virus) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P11124
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
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: 1

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Sample preparation

CrystalDensity Matthews: 2.92 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: BM14 / Wavelength: 0.9724
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 15, 2000 / Details: TOROIDAL MIRROR
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 2.9→20 Å / Num. obs: 56000 / % possible obs: 95 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 7.1
Reflection shellResolution: 2.9→3 Å / Rmerge(I) obs: 0.96 / Mean I/σ(I) obs: 1.1 / % possible all: 86
Reflection shell
*PLUS
% possible obs: 86 %

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY TBA

Resolution: 2.9→20 Å / Data cutoff high absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.271 2799 5 %RANDOM
Rwork0.237 ---
obs0.237 55386 94.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 22 Å2 / ksol: 0.316 e/Å3
Displacement parametersBiso mean: 51 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å23.6 Å2
2---23.4 Å20 Å2
3---23.3 Å2
Refine analyzeLuzzati d res low obs: 20 Å
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15795 285 3 0 16083
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
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_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.73
X-RAY DIFFRACTIONc_mcangle_it5.54
X-RAY DIFFRACTIONc_scbond_it6.74
X-RAY DIFFRACTIONc_scangle_it9.45
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2DNA-RNA_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM

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