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- PDB-4a8k: Non-Catalytic Ions Direct the RNA-Dependent RNA Polymerase of Bac... -

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Basic information

Entry
Database: PDB / ID: 4a8k
TitleNon-Catalytic Ions Direct the RNA-Dependent RNA Polymerase of Bacterial dsRNA virus phi6 from De Novo Initiation to Elongation
Components
  • 5'-D(*AP*AP*TP*CP)-3'
  • 5'-D(*TP*CP)-3'
  • RNA-DIRECTED RNA POLYMERASE
KeywordsTRANSFERASE/DNA / TRANSFERASE-DNA COMPLEX / TRANSFERASE
Function / homology
Function and homology information


RNA uridylyltransferase activity / virion component / RNA-directed RNA polymerase / viral RNA genome replication / RNA-directed 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)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 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 1.1May 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
A: RNA-DIRECTED RNA POLYMERASE
B: RNA-DIRECTED RNA POLYMERASE
C: RNA-DIRECTED RNA POLYMERASE
E: 5'-D(*AP*AP*TP*CP)-3'
F: 5'-D(*TP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,46911
Polymers226,8265
Non-polymers1,6426
Water00
1
A: RNA-DIRECTED RNA POLYMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,5823
Polymers75,0341
Non-polymers5472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RNA-DIRECTED RNA POLYMERASE
E: 5'-D(*AP*AP*TP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,7574
Polymers76,2092
Non-polymers5472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: RNA-DIRECTED RNA POLYMERASE
F: 5'-D(*TP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,1304
Polymers75,5832
Non-polymers5472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)106.530, 93.028, 140.860
Angle α, β, γ (deg.)90.00, 101.36, 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 (bacteriophage) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P11124, RNA-directed RNA polymerase
#2: DNA chain 5'-D(*AP*AP*TP*CP)-3'


Mass: 1174.831 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: DNA chain 5'-D(*TP*CP)-3'


Mass: 548.417 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#4: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 523.180 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM

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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: 3.02 Å3/Da / Density % sol: 59.23 % / 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: 2.9→58.7 Å / Num. obs: 55288 / % possible obs: 95 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 52.59 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.7

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Processing

SoftwareName: BUSTER / Version: 2.9.2 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→46.51 Å / Cor.coef. Fo:Fc: 0.8714 / Cor.coef. Fo:Fc free: 0.8502 / Cross valid method: THROUGHOUT / σ(F): 0
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=MG GTP. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=15909. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=96. ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=MG GTP. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=15909. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=96. NUMBER TREATED BY BAD NON-BONDED CONTACTS=3. DISORDERED REGIONS WERE MODELED STEREOCHEICALLY. (-AUTONCS).
RfactorNum. reflection% reflectionSelection details
Rfree0.3072 1726 5.1 %RANDOM
Rwork0.2763 ---
obs0.2778 34141 95 %-
Displacement parametersBiso mean: 98.57 Å2
Baniso -1Baniso -2Baniso -3
1-17.0623 Å20 Å26.0158 Å2
2---52.3178 Å20 Å2
3---35.2555 Å2
Refinement stepCycle: LAST / Resolution: 3.5→46.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15795 114 99 0 16008
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00816416HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0322249HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5746SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes384HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2379HARMONIC5
X-RAY DIFFRACTIONt_it16416HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.74
X-RAY DIFFRACTIONt_other_torsion17.93
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2022SEMIHARMONIC5
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_contact18371SEMIHARMONIC4
LS refinement shellResolution: 3.5→3.61 Å / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.5051 163 5.86 %
Rwork0.4834 2619 -
all0.4847 2782 -
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)
10.85360.30320.02410.49250.07120.7596-0.00070.23030.0384-0.06120.0658-0.01880.0261-0.0474-0.0651-0.11650.0169-0.13130.16340.0197-0.18579.3657-0.306728.3772
20.45120.28750.62020.69090.31760.8380.01550.0842-0.07570.00980.0259-0.0260.01420.0895-0.0414-0.07990.0756-0.08310.1074-0.0855-0.186258.878120.587355.9104
30.6347-0.2449-0.21050.64020.49992.2107-0.03460.0023-0.0359-0.0518-0.00790.07-0.2295-0.1620.0425-0.04780.0311-0.1272-0.0986-0.025-0.2168-42.80282.3678-3.4124
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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