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- PDB-4kbg: almost closed conformation of the helicase core of the RNA helica... -

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Basic information

Entry
Database: PDB / ID: 4kbg
Titlealmost closed conformation of the helicase core of the RNA helicase Hera
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 / 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 / helicase superfamily 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 / 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: 2.54 Å
AuthorsRudolph, M.G. / Klostermeier, D.
CitationJournal: Biopolymers / Year: 2013
Title: Rearranging RNA structures at 75C? toward the molecular mechanism and physiological function of the thermus thermophilus DEAD-box helicase hera.
Authors: Klostermeier, D.
History
DepositionApr 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Sep 20, 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)80,5768
Polymers80,0002
Non-polymers5766
Water99155
1
A: Heat resistant RNA dependent ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1923
Polymers40,0001
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Heat resistant RNA dependent ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3845
Polymers40,0001
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-107 kcal/mol
Surface area24780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.200, 128.702, 101.761
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Detailsthe core is monomeric while the intact Hera is a dimer

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Components

#1: Protein Heat resistant RNA dependent ATPase


Mass: 39999.945 Da / Num. of mol.: 2 / Fragment: helicase core
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB27 / ATCC BAA-163 / DSM 7039 / Gene: TT_C1895 / Production host: Escherichia coli (E. coli) / References: UniProt: Q72GF3
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.6 Å3/Da / Density % sol: 52.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99997 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99997 Å / Relative weight: 1
ReflectionResolution: 2.54→45.24 Å / Num. obs: 27922 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.66 % / Biso Wilson estimate: 58.7 Å2 / Rsym value: 0.1615 / Net I/σ(I): 8.19
Reflection shellResolution: 2.54→2.64 Å / Redundancy: 6.63 % / Mean I/σ(I) obs: 1.03 / Num. unique all: 3003 / Rsym value: 0.8254 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: dev_1327)refinement
XDSdata reduction
SADABSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2gxs, 2db3

2gxs

2db3


Resolution: 2.54→44.348 Å / SU ML: 0.38 / σ(F): 1.34 / Phase error: 30.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2375 1400 5.02 %random
Rwork0.1858 ---
obs0.1884 27867 99.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.54→44.348 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4384 0 30 55 4469
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084482
X-RAY DIFFRACTIONf_angle_d1.1426083
X-RAY DIFFRACTIONf_dihedral_angle_d14.6871708
X-RAY DIFFRACTIONf_chiral_restr0.071705
X-RAY DIFFRACTIONf_plane_restr0.005793
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.54-2.63080.3711290.33532610X-RAY DIFFRACTION99
2.6308-2.73610.37431210.31952633X-RAY DIFFRACTION100
2.7361-2.86060.38121340.29552606X-RAY DIFFRACTION100
2.8606-3.01140.33081320.26322645X-RAY DIFFRACTION100
3.0114-3.20.31421630.242581X-RAY DIFFRACTION100
3.2-3.4470.27021320.21672649X-RAY DIFFRACTION100
3.447-3.79370.21811540.17122633X-RAY DIFFRACTION100
3.7937-4.34230.22221470.13992638X-RAY DIFFRACTION100
4.3423-5.46920.16021370.12152690X-RAY DIFFRACTION100
5.4692-44.35480.1761510.15092782X-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)
16.10392.42621.91685.51281.42674.83440.1285-0.4730.14220.4396-0.1692-0.19690.09850.37110.03860.4996-0.00340.00720.37440.04220.3657-15.177714.404232.6861
25.6849-1.931-0.75563.1608-0.77666.1573-0.01660.12550.09890.2901-0.1771-0.3347-0.03920.45340.18430.3701-0.0865-0.05370.2787-0.04190.2961-12.431623.354920.3267
32.6817-2.76344.51726.5862-3.87327.7951-0.3251-0.16130.39460.8973-0.01680.15-0.5762-0.21250.25410.297-0.0512-0.00240.3538-0.06490.3634-15.981529.588925.6484
47.8368-5.8628-3.22486.9260.79675.78330.46650.14341.096-0.139-0.316-0.2264-0.84120.1128-0.11920.45320.0295-0.07190.3249-0.03640.4437-16.543339.199114.9268
50.33570.3495-1.39442.7318-0.17956.4134-0.12930.3763-0.1617-0.0876-0.21880.0781-0.2899-0.15780.36460.29810.0241-0.03210.37020.00910.4646-20.111231.307112.8276
64.9531-1.6482.90536.2219-1.18413.00230.0462-0.2213-0.1592-0.20280.02480.08080.08630.0565-0.08940.3658-0.0254-0.01780.1526-0.0620.2026-23.511324.471415.2046
76.9182-1.7792-5.59728.53532.10554.5867-0.01980.9851-0.3492-0.3509-0.03770.55440.0057-0.7729-0.01050.499-0.0111-0.15530.41870.02580.3628-27.754422.85659.2778
82.91311.0587-2.11542.0033-2.06464.9128-0.06480.2601-0.0912-0.01420.21410.30710.6164-0.2681-0.09740.47990.0097-0.03850.2789-0.01980.3363-27.144712.666418.0119
91.45680.38160.43573.1596-0.36572.03590.14-0.09730.0070.1144-0.1143-0.0905-0.13520.1352-0.01720.4724-0.03010.04880.3140.00120.3087-24.8309-11.567235.6095
106.5534-1.1438-1.21585.28231.52255.4437-0.0955-0.3299-0.06290.42480.0679-0.2161-0.31340.37370.03490.6579-0.0266-0.03640.36990.03990.2935-21.5311-23.271712.6093
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 50 )
2X-RAY DIFFRACTION2chain 'A' and (resid 51 through 81 )
3X-RAY DIFFRACTION3chain 'A' and (resid 82 through 104 )
4X-RAY DIFFRACTION4chain 'A' and (resid 105 through 119 )
5X-RAY DIFFRACTION5chain 'A' and (resid 120 through 136 )
6X-RAY DIFFRACTION6chain 'A' and (resid 137 through 161 )
7X-RAY DIFFRACTION7chain 'A' and (resid 162 through 171 )
8X-RAY DIFFRACTION8chain 'A' and (resid 172 through 207 )
9X-RAY DIFFRACTION9chain 'B' and (resid 1 through 224 )
10X-RAY DIFFRACTION10chain 'B' and (resid 225 through 365 )

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