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- PDB-4kbf: two different open conformations of the helicase core of the RNA ... -

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Basic information

Entry
Database: PDB / ID: 4kbf
Titletwo different open conformations 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / Heat resistant RNA dependent ATPase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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

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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)80,4896
Polymers80,0002
Non-polymers4894
Water2,864159
1
A: Heat resistant RNA dependent ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3934
Polymers40,0001
Non-polymers3933
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Heat resistant RNA dependent ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0962
Polymers40,0001
Non-polymers961
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 area2830 Å2
ΔGint-53 kcal/mol
Surface area32630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.645, 119.645, 107.095
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
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-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 2.4 Å3/Da / Density % sol: 48.65 %
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: 0.9788 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 5, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 1.9→48.88 Å / Num. obs: 61258 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.01 % / Biso Wilson estimate: 37.3 Å2 / Rsym value: 0.0719 / Net I/σ(I): 18.7
Reflection shellResolution: 1.9→2 Å / Redundancy: 12.73 % / Mean I/σ(I) obs: 1.58 / Num. unique all: 8492 / Rsym value: 0.8172 / % possible all: 98.4

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Processing

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

2gxq

2db3


Resolution: 1.9→48.876 Å / SU ML: 0.24 / σ(F): 1.33 / Phase error: 23.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2184 3119 5.1 %random
Rwork0.1904 ---
obs0.1918 61164 99.26 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→48.876 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5630 0 30 159 5819
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065762
X-RAY DIFFRACTIONf_angle_d0.9777817
X-RAY DIFFRACTIONf_dihedral_angle_d14.6062218
X-RAY DIFFRACTIONf_chiral_restr0.061897
X-RAY DIFFRACTIONf_plane_restr0.0051031
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.92970.44621370.36952511X-RAY DIFFRACTION97
1.9297-1.96130.32471340.27492595X-RAY DIFFRACTION99
1.9613-1.99520.27631470.24252562X-RAY DIFFRACTION99
1.9952-2.03140.27771620.23962570X-RAY DIFFRACTION99
2.0314-2.07050.29691360.24412582X-RAY DIFFRACTION99
2.0705-2.11280.25641290.2192608X-RAY DIFFRACTION99
2.1128-2.15870.24091370.20732589X-RAY DIFFRACTION99
2.1587-2.20890.24451470.19732613X-RAY DIFFRACTION99
2.2089-2.26420.24751220.19832620X-RAY DIFFRACTION99
2.2642-2.32540.2291440.19222623X-RAY DIFFRACTION99
2.3254-2.39380.19961380.19312630X-RAY DIFFRACTION99
2.3938-2.47110.28641410.19432620X-RAY DIFFRACTION99
2.4711-2.55940.24381330.20622625X-RAY DIFFRACTION99
2.5594-2.66190.21251370.20452649X-RAY DIFFRACTION100
2.6619-2.7830.22561340.20762663X-RAY DIFFRACTION100
2.783-2.92970.26331340.20322649X-RAY DIFFRACTION100
2.9297-3.11320.1991720.20132624X-RAY DIFFRACTION100
3.1132-3.35350.22721390.19042679X-RAY DIFFRACTION100
3.3535-3.69090.17721370.17732700X-RAY DIFFRACTION100
3.6909-4.22470.21781550.17162698X-RAY DIFFRACTION100
4.2247-5.32170.17571600.15962724X-RAY DIFFRACTION100
5.3217-48.89190.21571440.18662911X-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)
11.0513-0.16360.3591.10350.04563.3333-0.07260.05630.0202-0.0917-0.0941-0.0638-0.02190.45780.14350.1638-0.02910.00480.25730.05770.234317.8015-47.5538-13.3779
23.6516-0.11460.34075.7323-0.40843.31450.0127-0.65690.1770.4130.0806-0.0212-0.0038-0.1954-0.08250.302-0.10050.00280.3712-0.05310.231935.1541-22.5722-2.5693
31.03030.0894-0.11691.7872-0.29912.2582-0.0436-0.17710.26120.27170.03970.13-0.2806-0.06450.00610.2780.03820.00060.3003-0.05550.33048.2183-41.108321.401
45.8143-1.74430.54873.3673-0.18191.87810.1851-0.38340.35660.57230.0747-1.3342-0.39540.3149-0.21551.05160.1563-0.17930.9255-0.04351.307-7.3901-10.1319-19.3882
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resid 1:207)
2X-RAY DIFFRACTION2chain A and (resid 208:365)
3X-RAY DIFFRACTION3chain B and (resid 1:207)
4X-RAY DIFFRACTION4chain B and (resid 212:365)

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