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- PDB-3ber: Human DEAD-box RNA-helicase DDX47, conserved domain I in complex ... -

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Basic information

Entry
Database: PDB / ID: 3ber
TitleHuman DEAD-box RNA-helicase DDX47, conserved domain I in complex with AMP
ComponentsProbable ATP-dependent RNA helicase DDX47
KeywordsHYDROLASE / RNA HELICASE / DEAD / AMP / Structural Genomics / Structural Genomics Consortium / SGC / ATP-binding / Nucleotide-binding / Nucleus / RNA-binding
Function / homology
Function and homology information


rRNA modification in the nucleus and cytosol / extrinsic apoptotic signaling pathway via death domain receptors / Major pathway of rRNA processing in the nucleolus and cytosol / RNA splicing / mRNA processing / rRNA processing / RNA helicase activity / RNA helicase / nucleolus / ATP hydrolysis activity ...rRNA modification in the nucleus and cytosol / extrinsic apoptotic signaling pathway via death domain receptors / Major pathway of rRNA processing in the nucleolus and cytosol / RNA splicing / mRNA processing / rRNA processing / RNA helicase activity / RNA helicase / nucleolus / ATP hydrolysis activity / RNA binding / nucleoplasm / ATP binding / nucleus / membrane
Similarity search - Function
DDX47/Rrp3, DEAD-box helicase 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 domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain ...DDX47/Rrp3, DEAD-box helicase 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 domain / DEAD/DEAH box helicase / 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 / TRIETHYLENE GLYCOL / PHOSPHATE ION / Probable ATP-dependent RNA helicase DDX47
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsKarlberg, T. / Busam, R.D. / Arrowsmith, C.H. / Berglund, H. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. ...Karlberg, T. / Busam, R.D. / Arrowsmith, C.H. / Berglund, H. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, I. / Kallas, A. / Kotenyova, T. / Lehtio, L. / Moche, M. / Nilsson, M.E. / Nordlund, P. / Nyman, T. / Persson, C. / Sagemark, J. / Svensson, L. / Thorsell, A.G. / Tresaugues, L. / Van Den Berg, S. / Weigelt, J. / Welin, M. / Holmberg-Schiavone, L. / Structural Genomics Consortium (SGC)
CitationJournal: Plos One / Year: 2010
Title: Comparative Structural Analysis of Human DEAD-Box RNA Helicases.
Authors: Schutz, P. / Karlberg, T. / van den Berg, S. / Collins, R. / Lehtio, L. / Hogbom, M. / Holmberg-Schiavone, L. / Tempel, W. / Park, H.W. / Hammarstrom, M. / Moche, M. / Thorsell, A.G. / Schuler, H.
History
DepositionNov 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable ATP-dependent RNA helicase DDX47
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2035
Polymers27,4611
Non-polymers7434
Water5,386299
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.050, 70.370, 35.860
Angle α, β, γ (deg.)90.00, 90.70, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-498-

HOH

21A-672-

HOH

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Components

#1: Protein Probable ATP-dependent RNA helicase DDX47 / DEAD box protein 47


Mass: 27460.580 Da / Num. of mol.: 1 / Fragment: Conserved domain I (DEAD): Residues 5-230
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDX47 / Plasmid: pNIC-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)gold pRARE2
References: UniProt: Q9H0S4, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / 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: 2.14 Å3/Da / Density % sol: 42.46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.2
Details: 42.5% PEG 200, 100mM Sodium/potassium phosphate, 50mM Sodium chloride, pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97472 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 25, 2007
Details: liquid nitrogen cooled channel-cut silicon monochromator and a cylindrical grazing incidence mirror
RadiationMonochromator: Si(311) and Si(111) crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97472 Å / Relative weight: 1
ReflectionResolution: 1.4→30 Å / Num. all: 45260 / Num. obs: 45260 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rmerge(I) obs: 0.052 / Rsym value: 0.029 / Net I/σ(I): 28.7
Reflection shellResolution: 1.4→1.5 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.141 / Mean I/σ(I) obs: 14.1 / Num. unique all: 8478 / Rsym value: 0.082 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.3.0040refinement
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2GXS

2gxs


Resolution: 1.4→28.24 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.956 / SU B: 0.833 / SU ML: 0.035 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.058 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18914 2274 5 %RANDOM
Rwork0.1654 ---
all0.16659 43193 --
obs0.16659 43193 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.83 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20.04 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.4→28.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1688 0 48 299 2035
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221836
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6382.0252497
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8485241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.76925.44168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.64615345
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.09159
X-RAY DIFFRACTIONr_chiral_restr0.0940.2301
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021317
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2230.2922
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21312
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1980.2237
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.5270.289
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3130.251
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0531.51169
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.69721871
X-RAY DIFFRACTIONr_scbond_it2.713725
X-RAY DIFFRACTIONr_scangle_it4.3074.5620
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.226 169 -
Rwork0.195 3207 -
obs--100 %

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