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- PDB-3i32: Dimeric structure of a Hera helicase fragment including the C-ter... -

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Basic information

Entry
Database: PDB / ID: 3i32
TitleDimeric structure of a Hera helicase fragment including the C-terminal RecA domain, the dimerization domain, and the RNA binding domain
ComponentsHeat resistant RNA dependent ATPase
KeywordsRNA BINDING PROTEIN / Hydrolase / RNA helicase / ATPase / Dimer / 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
: / 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
BROMIDE ION / Heat resistant RNA dependent ATPase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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: Refinement description / Category: software
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heat resistant RNA dependent ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5823
Polymers33,4221
Non-polymers1602
Water00
1
A: Heat resistant RNA dependent ATPase
hetero molecules

A: Heat resistant RNA dependent ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,1646
Polymers66,8452
Non-polymers3204
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area4060 Å2
ΔGint-43 kcal/mol
Surface area28600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.960, 64.960, 153.564
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: 33422.383 Da / Num. of mol.: 1 / Fragment: residues 218-517
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-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 5

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.25 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.5
Details: 0.1 M MES-NaOH pH 6.5, 15-18% ethylene glycol, 0.3-0.5 M NaCl, 3-6% PEG 20 000, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 18, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.5→39.42 Å / Num. obs: 12078 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 50 % / Biso Wilson estimate: 100 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 28.2
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 51.6 % / Rmerge(I) obs: 0.911 / Mean I/σ(I) obs: 1.9 / Num. unique all: 679 / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine)refinement
XDSdata reduction
SADABSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Hera RBD and 2eaq

2eaq


Resolution: 2.8→39.42 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.83 / σ(F): 0.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2925 732 4.83 %random
Rwork0.2533 ---
obs0.2553 12022 98.1 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 84.992 Å2 / ksol: 0.333 e/Å3
Displacement parametersBiso max: 211.75 Å2 / Biso mean: 118.83 Å2 / Biso min: 50.48 Å2
Baniso -1Baniso -2Baniso -3
1--16.252 Å2-0 Å20 Å2
2---16.252 Å20 Å2
3---15.365 Å2
Refinement stepCycle: LAST / Resolution: 2.8→39.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2162 0 2 0 2164
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082201
X-RAY DIFFRACTIONf_angle_d1.1552977
X-RAY DIFFRACTIONf_dihedral_angle_d17.369840
X-RAY DIFFRACTIONf_chiral_restr0.069327
X-RAY DIFFRACTIONf_plane_restr0.005397
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-3.01630.35861260.32792766X-RAY DIFFRACTION94
3.0163-3.31970.37711520.30142875X-RAY DIFFRACTION98
3.3197-3.79970.37061500.29592923X-RAY DIFFRACTION100
3.7997-4.78590.31451320.23982962X-RAY DIFFRACTION100
4.7859-39.42230.23391720.22592910X-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)
13.76250.70362.12283.09190.48784.1976-0.0979-1.29680.1136-0.0056-0.18180.2432-0.2836-1.39350.32960.5880.0703-0.03741.0363-0.22660.5508-19.6212-28.8579-16.0788
20.68050.570.46612.06791.44372.58210.07680.101-0.1361-0.23660.1515-0.1547-0.1604-0.0203-0.22920.60030.02330.00390.675-0.22180.802-8.4478-20.4417-13.4835
31.4461-1.01520.26262.74010.34882.22650.03640.08931.8468-0.6554-0.7972-1.8408-0.17130.55640.76260.85010.08490.38110.7923-0.04531.310913.3789-38.7199-10.6465
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and (resid 211:318)A211 - 318
2X-RAY DIFFRACTION2chain A and (resid 319:424)A319 - 424
3X-RAY DIFFRACTION3chain A and (resid 425:491)A425 - 491

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