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- PDB-3i31: Hera helicase RNA binding domain is an RRM fold -

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Basic information

Entry
Database: PDB / ID: 3i31
TitleHera helicase RNA binding domain is an RRM fold
ComponentsHeat resistant RNA dependent ATPase
KeywordsRNA BINDING PROTEIN / HYDROLASE / RNA helicase / RNA recognition motif / 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
Alpha-Beta Plaits - #1800 / : / 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 ...Alpha-Beta Plaits - #1800 / : / 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 / Alpha-Beta Plaits / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Heat resistant RNA dependent ATPase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.8 Å
AuthorsRudolph, M.G. / Klostermeier, D.
CitationJournal: Rna / Year: 2009
Title: The Thermus thermophilus DEAD box helicase Hera contains a modified RNA recognition motif domain loosely connected to the helicase core.
Authors: Rudolph, M.G. / Klostermeier, D.
History
DepositionJun 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Data collection / Refinement description / Category: diffrn / refine / software / Item: _refine.pdbx_ls_cross_valid_method
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,9066
Polymers9,6491
Non-polymers2575
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.516, 37.516, 136.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Heat resistant RNA dependent ATPase


Mass: 9649.090 Da / Num. of mol.: 1 / Fragment: residues 431-517
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) / References: UniProt: Q72GF3
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.5 Å3/Da / Density % sol: 50.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M NaCac pH 6.5, 16-18% P8000, 0.3-0.4M Zn(OAc)2, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSLS X06SA11
SYNCHROTRONSLS X06DA21.8
Detector
TypeIDDetectorDate
PSI PILATUS 6M1PIXELJun 5, 2009
MARMOSAIC 225 mm CCD2CCDJun 5, 2009
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.81
ReflectionResolution: 1.8→36.18 Å / Num. obs: 9812 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 28 Å2 / Rsym value: 0.122 / Net I/σ(I): 7.5
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 1.6 / Num. unique all: 457 / Rsym value: 0.706 / % possible all: 100

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Processing

Software
NameVersionClassification
SHELXDEphasing
PHENIX(phenix.refine)refinement
XDSdata reduction
SADABSdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 1.8→34.222 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 1.43 / Cross valid method: FREE R-VALUE / σ(F): 0.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2235 427 4.81 %random
Rwork0.2003 ---
obs0.2015 8882 90.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.721 Å2 / ksol: 0.358 e/Å3
Displacement parametersBiso max: 118.51 Å2 / Biso mean: 42.653 Å2 / Biso min: 19.66 Å2
Baniso -1Baniso -2Baniso -3
1-6.423 Å20 Å2-0 Å2
2--6.423 Å2-0 Å2
3----12.846 Å2
Refinement stepCycle: LAST / Resolution: 1.8→34.222 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms581 0 12 39 632
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008597
X-RAY DIFFRACTIONf_angle_d1.202805
X-RAY DIFFRACTIONf_dihedral_angle_d17.462230
X-RAY DIFFRACTIONf_chiral_restr0.06888
X-RAY DIFFRACTIONf_plane_restr0.007105
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-2.06050.27281400.22452346X-RAY DIFFRACTION79
2.0605-2.59580.2481430.17782856X-RAY DIFFRACTION94
2.5958-34.22870.20791440.20283253X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 6.2174 Å / Origin y: 19.7902 Å / Origin z: 23.2016 Å
111213212223313233
T0.2971 Å2-0.0126 Å2-0.0511 Å2-0.1741 Å2-0.0034 Å2--0.2421 Å2
L1.3984 °20.0797 °2-0.9918 °2-0.78 °20.8351 °2--0.6232 °2
S0.0127 Å °-0.1116 Å °-0.1361 Å °-0.0477 Å °0.0318 Å °0.1596 Å °0.2014 Å °-0.2157 Å °0 Å °
Refinement TLS groupSelection details: chain A

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