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- PDB-3eaq: Novel dimerization motif in the DEAD box RNA helicase Hera form 2... -

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Basic information

Entry
Database: PDB / ID: 3eaq
TitleNovel dimerization motif in the DEAD box RNA helicase Hera form 2, complete dimer, symmetric
ComponentsHeat resistant RNA dependent ATPase
KeywordsHYDROLASE / DEAD box RNA helicase / dimer / ATP-binding / Helicase / Nucleotide-binding
Function / homology
Function and homology information


nucleic acid binding / RNA helicase activity / hydrolase activity / ATP binding / metal ion binding
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #710 / : / RNA helicase Hera, dimerization domain / DEAD box helicase Hera, RNA-binding domain / : / DEAD-box subfamily ATP-dependent helicases signature. / RNA helicase, DEAD-box type, Q motif / ATP-dependent RNA helicase DEAD-box, conserved site / DEAD-box RNA helicase Q motif profile. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #710 / : / RNA helicase Hera, dimerization domain / DEAD box helicase Hera, RNA-binding domain / : / DEAD-box subfamily ATP-dependent helicases signature. / RNA helicase, DEAD-box type, Q motif / ATP-dependent RNA helicase DEAD-box, conserved site / DEAD-box RNA helicase Q motif profile. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helix non-globular / Helicase conserved C-terminal domain / Special / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Heat resistant RNA dependent ATPase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKlostermeier, D. / Rudolph, M.G.
CitationJournal: Nucleic Acids Res. / Year: 2009
Title: A novel dimerization motif in the C-terminal domain of the Thermus thermophilus DEAD box helicase Hera confers substantial flexibility.
Authors: Klostermeier, D. / Rudolph, M.G.
History
DepositionAug 26, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heat resistant RNA dependent ATPase
B: Heat resistant RNA dependent ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8054
Polymers47,7352
Non-polymers712
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-57 kcal/mol
Surface area21950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.620, 70.780, 101.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Heat resistant RNA dependent ATPase


Mass: 23867.275 Da / Num. of mol.: 2 / Fragment: internal fragment (UNP residues 215 to 426)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB27 / Gene: TT_C1895 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: Q72GF3
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.37 Å3/Da / Density % sol: 48.01 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 8.5
Details: PEG3350, ammonium sulfate, pH 8.5, microbatch, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 31, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→46.9 Å / Num. all: 20794 / Num. obs: 20794 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.8 % / Biso Wilson estimate: 57.914 Å2 / Rsym value: 0.106 / Net I/σ(I): 12.9
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 10.3 % / Mean I/σ(I) obs: 1.7 / Num. unique all: 772 / Rsym value: 0.95 / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
BUSTER-TNT2.5.1refinement
XDSdata reduction
SADABSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: crude model built in MAD/phased maps from a tetragonal crystal form

Resolution: 2.3→46.88 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.269 1064 5.13 %RANDOM
Rwork0.218 ---
obs0.2207 20745 99.82 %-
Displacement parametersBiso mean: 66.45 Å2
Baniso -1Baniso -2Baniso -3
1-8.64526908 Å20 Å20 Å2
2--7.96593968 Å20 Å2
3----16.61120876 Å2
Refinement stepCycle: LAST / Resolution: 2.3→46.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3305 0 2 7 3314
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.00733552
X-RAY DIFFRACTIONt_angle_deg1.06945182
X-RAY DIFFRACTIONt_dihedral_angle_d28.9497240
X-RAY DIFFRACTIONt_trig_c_planes0.007772
X-RAY DIFFRACTIONt_gen_planes0.0125085
X-RAY DIFFRACTIONt_it1.604335520
X-RAY DIFFRACTIONt_nbd0.0471225
LS refinement shellResolution: 2.3→2.44 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.3157 173 5.27 %
Rwork0.2855 3107 -
all0.287 3280 -
obs--99.82 %

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