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- PDB-3agq: Structure of viral polymerase form II -

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Basic information

Entry
Database: PDB / ID: 3agq
TitleStructure of viral polymerase form II
ComponentsElongation factor Ts, Elongation factor Tu 1, LINKER, Q beta replicase
KeywordsTRANSLATION / TRANSFERASE / RNA polymerase / replicase
Function / homology
Function and homology information


protein-synthesizing GTPase / guanosine tetraphosphate binding / translation elongation factor activity / RNA-directed RNA polymerase / response to antibiotic / viral RNA genome replication / nucleotide binding / RNA-directed RNA polymerase activity / GTPase activity / GTP binding ...protein-synthesizing GTPase / guanosine tetraphosphate binding / translation elongation factor activity / RNA-directed RNA polymerase / response to antibiotic / viral RNA genome replication / nucleotide binding / RNA-directed RNA polymerase activity / GTPase activity / GTP binding / RNA binding / metal ion binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
RNA-directed RNA polymerase beta-chain / RNA replicase, beta-chain / Translation elongation factor EFTs/EF1B / Translation elongation factor EFTs/EF1B, dimerisation / Translation elongation factor Ts, conserved site / Elongation factor Ts, dimerisation domain superfamily / Elongation factor TS / Elongation factor Ts signature 1. / Elongation factor Ts signature 2. / RNA-directed RNA polymerase, bacteriophage, catalytic domain ...RNA-directed RNA polymerase beta-chain / RNA replicase, beta-chain / Translation elongation factor EFTs/EF1B / Translation elongation factor EFTs/EF1B, dimerisation / Translation elongation factor Ts, conserved site / Elongation factor Ts, dimerisation domain superfamily / Elongation factor TS / Elongation factor Ts signature 1. / Elongation factor Ts signature 2. / RNA-directed RNA polymerase, bacteriophage, catalytic domain / RdRp of RNA-containing bacteriophages catalytic domain profile. / Translation elongation factor EFTu/EF1A, C-terminal / Translation elongation factor EFTu/EF1A, bacterial/organelle / Elongation factor Tu, domain 2 / Elongation factor Tu (EF-Tu), GTP-binding domain / : / Elongation factor Tu C-terminal domain / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / UBA-like superfamily / Translation factors / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Elongation Factor Tu (Ef-tu); domain 3 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / P-loop containing nucleotide triphosphate hydrolases / DNA/RNA polymerase superfamily / Beta Barrel / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Elongation factor Tu / Elongation factor Ts / RNA-directed RNA polymerase subunit beta
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
synthetic construct (others)
Escherichia phage Qbeta (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.22 Å
AuthorsTakeshita, D. / Tomita, K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Assembly of Q{beta} viral RNA polymerase with host translational elongation factors EF-Tu and -Ts
Authors: Takeshita, D. / Tomita, K.
History
DepositionApr 6, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 29, 2014Group: Database references
Revision 1.3Jun 28, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.4Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_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_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Elongation factor Ts, Elongation factor Tu 1, LINKER, Q beta replicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,4422
Polymers141,4181
Non-polymers241
Water724
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Elongation factor Ts, Elongation factor Tu 1, LINKER, Q beta replicase
hetero molecules

A: Elongation factor Ts, Elongation factor Tu 1, LINKER, Q beta replicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)282,8844
Polymers282,8352
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area2120 Å2
ΔGint-11 kcal/mol
Surface area104350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.769, 255.119, 100.975
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Elongation factor Ts, Elongation factor Tu 1, LINKER, Q beta replicase


Mass: 141417.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria), (gene. exp.) synthetic construct (others), (gene. exp.) Escherichia phage Qbeta (virus)
Plasmid: pBAD33 / Production host: Escherichia coli (E. coli)
References: UniProt: P0A6P3, UniProt: P0A6N3, UniProt: Q8LTE0
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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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: 3.16 Å3/Da / Density % sol: 61.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 32% PEG400, 0.2M magnesium acetate, 0.1M HEPES, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 11, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.2→30 Å / Num. obs: 28658 / % possible obs: 98.5 % / Redundancy: 8.4 % / Rmerge(I) obs: 0.107
Reflection shellResolution: 3.2→3.26 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.341 / Num. unique all: 1396 / % possible all: 98.1

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Processing

Software
NameClassification
HKL-2000data collection
MOLREPphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AGP

3agp


Resolution: 3.22→20 Å
RfactorNum. reflection% reflection
Rfree0.317 1444 -
Rwork0.251 --
obs-28539 97.6 %
Refinement stepCycle: LAST / Resolution: 3.22→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9252 0 1 4 9257
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_refined_d0.005
X-RAY DIFFRACTIONf_angle_refined_deg0.769
LS refinement shellResolution: 3.2213→3.2414 Å / Rfactor Rwork: 0.476

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