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- PDB-3nej: Q28E mutant of Hera RNA helicase N-terminal domain - perfectly tw... -

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Basic information

Entry
Database: PDB / ID: 3nej
TitleQ28E mutant of Hera RNA helicase N-terminal domain - perfectly twinned hexagonal form
ComponentsHeat resistant RNA dependent ATPase
KeywordsHYDROLASE / RNA HELICASE / RIBOSOME BIOGENESIS / THERMOPHILIC / ATPASE
Function / homology
Function and homology information


nucleic acid binding / RNA helicase activity / hydrolase activity / ATP binding / metal ion binding / cytosol
Similarity search - Function
: / 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. / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Helicase conserved C-terminal domain ...: / 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. / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Helicase conserved C-terminal domain / 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: 2.57 Å
AuthorsRudolph, M.G.
CitationJournal: Biol.Chem. / Year: 2011
Title: Changing nucleotide specificity of the DEAD-box helicase Hera abrogates communication between the Q-motif and the P-loop.
Authors: Strohmeier, J. / Hertel, I. / Diederichsen, U. / Rudolph, M.G. / Klostermeier, D.
History
DepositionJun 9, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 27, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Nov 1, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)44,6882
Polymers44,6882
Non-polymers00
Water543
1
A: Heat resistant RNA dependent ATPase


Theoretical massNumber of molelcules
Total (without water)22,3441
Polymers22,3441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Heat resistant RNA dependent ATPase


Theoretical massNumber of molelcules
Total (without water)22,3441
Polymers22,3441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.689, 59.689, 239.852
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Heat resistant RNA dependent ATPase


Mass: 22343.938 Da / Num. of mol.: 2 / Fragment: N-terminal recA-like domain / Mutation: Q28E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB27 / Gene: TT_C1895 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q72GF3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.76 Å3/Da / Density % sol: 55.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 15% PEG3350, 0.2M sodium malate, 0.1M HEPES/NaOH pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 31, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.57→43.4 Å / Num. obs: 15772 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 64.3 Å2 / Rsym value: 0.124 / Net I/σ(I): 7.2
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 1.2 / Num. unique all: 1515 / Rsym value: 0.659 / % possible all: 86.4

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.6_289)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GXS

2gxs


Resolution: 2.57→39.975 Å / σ(F): 0.04 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2685 812 5.38 %
Rwork0.2121 --
obs0.2143 15080 90.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.703 Å2 / ksol: 0.257 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.3825 Å2-0 Å20 Å2
2---7.3825 Å20 Å2
3---14.765 Å2
Refinement stepCycle: LAST / Resolution: 2.57→39.975 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3081 0 0 3 3084
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043133
X-RAY DIFFRACTIONf_angle_d0.8684252
X-RAY DIFFRACTIONf_dihedral_angle_d14.4931184
X-RAY DIFFRACTIONf_chiral_restr0.056507
X-RAY DIFFRACTIONf_plane_restr0.004548
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5716-2.76980.40321220.3265226770
2.7698-3.04790.40391590.3007263581
3.0479-3.48760.31041710.2484288288
3.4876-4.38890.23571570.2008313694
4.3889-22.75450.22571600.1676334395
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)
10.41610.241-0.1550.3027-0.09110.0593-0.04490.1785-0.0845-0.07390.0109-0.0845-0.0346-0.0671-0.01150.11590.07980.00570.2205-0.0654-0.0618-13.2829-11.064718.384
20.38090.14550.00140.19720.0020.40030.03050.10960.1325-0.04110.02820.05890.02140.0033-0.02160.06870.08970.03250.1060.04290.0677-14.4721-43.427218.6051
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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