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

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Basic information

Entry
Database: PDB / ID: 3ear
TitleNovel dimerization motif in the DEAD box RNA helicase Hera: form 1, partial dimer
ComponentsHera
KeywordsHYDROLASE / DEAD box RNA helicase / dimer / ATP-binding / Helicase / Nucleotide-binding
Function / homology
Function and homology information


RNA helicase activity / nucleic acid binding / 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 subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #710 / : / RNA helicase Hera, dimerization domain / DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Helicase conserved C-terminal domain / Helix non-globular / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 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: Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hera
B: Hera


Theoretical massNumber of molelcules
Total (without water)47,7352
Polymers47,7352
Non-polymers00
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-39 kcal/mol
Surface area13700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.560, 67.720, 183.710
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 Hera


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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.71 Å3/Da / Density % sol: 54.58 %

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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: May 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 Å / Num. obs: 23978 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Rsym value: 0.048 / Net I/σ(I): 14.7
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 1375 / Rsym value: 0.661 / % possible all: 94.8

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine)refinement
XDSdata reduction
SADABSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3eaq

3eaq


Resolution: 2.3→45.928 Å / SU ML: 0.34 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2545 1186 4.99 %random
Rwork0.2306 ---
obs0.2317 22592 99.41 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 83.432 Å2 / ksol: 0.324 e/Å3
Refinement stepCycle: LAST / Resolution: 2.3→45.928 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2052 0 0 29 2081
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_deg0.92
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.40470.44031310.37872774X-RAY DIFFRACTION99
2.4047-2.53150.36241530.32142735X-RAY DIFFRACTION99
2.5315-2.69010.38261480.27752771X-RAY DIFFRACTION99
2.6901-2.89780.27781690.24142759X-RAY DIFFRACTION99
2.8978-3.18930.27771530.21282808X-RAY DIFFRACTION99
3.1893-3.65060.20931590.1972794X-RAY DIFFRACTION100
3.6506-4.59880.20771370.18162909X-RAY DIFFRACTION100
4.5988-45.93660.24451360.23583042X-RAY DIFFRACTION100
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)
11.2112-0.57810.62382.4544-0.12640.5475-0.1661-0.03040.36470.03540.1187-0.1478-0.04290.00510.05960.36610.0074-0.01870.3848-0.03590.454511.224127.555949.9611
21.3124-0.44281.07731.1023-0.5799-2.34990.1722-0.483-0.35061.34830.1459-0.26490.0733-0.349-0.23021.2214-0.0419-0.17430.7962-0.01490.440724.974913.517268.6326
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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