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- PDB-5ivl: CshA Helicase -

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Basic information

Entry
Database: PDB / ID: 5ivl
TitleCshA Helicase
ComponentsDEAD-box ATP-dependent RNA helicase CshA
KeywordsHYDROLASE / Rec-A like domain DEAD-box helicase
Function / homology
Function and homology information


RNA secondary structure unwinding / RNA catabolic process / RNA helicase activity / hydrolase activity / RNA helicase / RNA binding / ATP binding / cytoplasm
Similarity search - Function
DEAD-box ATP-dependent RNA helicase CshA / 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. ...DEAD-box ATP-dependent RNA helicase CshA / 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 nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DEAD-box ATP-dependent RNA helicase CshA
Similarity search - Component
Biological speciesGeobacillus stearothermophilus 10 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHuen, J. / Lin, C.-L. / Yi, W.-L. / Li, C.-L. / Yuan, H.
CitationJournal: Structure / Year: 2017
Title: Structural Insights into a Unique Dimeric DEAD-Box Helicase CshA that Promotes RNA Decay.
Authors: Huen, J. / Lin, C.-L. / Golzarroshan, B. / Yi, W.-L. / Yang, W.Z. / Yuan, H.S.
History
DepositionMar 21, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 8, 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

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Assembly

Deposited unit
B: DEAD-box ATP-dependent RNA helicase CshA
A: DEAD-box ATP-dependent RNA helicase CshA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,1266
Polymers96,7422
Non-polymers3844
Water3,765209
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-119 kcal/mol
Surface area37550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.489, 96.314, 83.773
Angle α, β, γ (deg.)90.00, 95.21, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DEAD-box ATP-dependent RNA helicase CshA


Mass: 48370.836 Da / Num. of mol.: 2 / Fragment: UNP residues 1-422
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus 10 (bacteria)
Gene: cshA, GT50_10605 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0K2H973, RNA helicase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 2.53 Å3/Da / Density % sol: 51.44 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 0.1M Sodium acetate, pH 4.6, 1.5M Ammonium sulfate

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 19, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→23.52 Å / Num. obs: 40920 / % possible obs: 99.7 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 32.84
Reflection shellResolution: 2.3→2.36 Å

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Processing

SoftwareName: PHENIX / Version: 1.8.1_1168 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HJV

2hjv


Resolution: 2.3→23.52 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 27.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.251 2056 5.03 %
Rwork0.202 --
obs0.205 40892 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.86 Å2
Refinement stepCycle: LAST / Resolution: 2.3→23.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6456 0 20 209 6685
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096567
X-RAY DIFFRACTIONf_angle_d1.1438861
X-RAY DIFFRACTIONf_dihedral_angle_d15.5412529
X-RAY DIFFRACTIONf_chiral_restr0.0751032
X-RAY DIFFRACTIONf_plane_restr0.0061143
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.302-2.35550.28111360.2132486X-RAY DIFFRACTION96
2.3555-2.41440.26481420.20732587X-RAY DIFFRACTION100
2.4144-2.47960.30031330.21412585X-RAY DIFFRACTION100
2.4796-2.55240.30141270.21652599X-RAY DIFFRACTION100
2.5524-2.63470.3051440.22262573X-RAY DIFFRACTION100
2.6347-2.72880.31271220.21872589X-RAY DIFFRACTION100
2.7288-2.83780.29311410.22222582X-RAY DIFFRACTION100
2.8378-2.96680.27711250.22572620X-RAY DIFFRACTION100
2.9668-3.12280.3191230.22572619X-RAY DIFFRACTION100
3.1228-3.3180.26891410.22612567X-RAY DIFFRACTION100
3.318-3.57340.23971190.19522608X-RAY DIFFRACTION100
3.5734-3.93150.2221510.19212593X-RAY DIFFRACTION100
3.9315-4.49690.20391530.17032585X-RAY DIFFRACTION100
4.4969-5.65260.21241450.18292599X-RAY DIFFRACTION100
5.6526-23.52040.25221540.20442644X-RAY DIFFRACTION100

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